{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"TODAY'S DATE:\n",
"Wed Jan 2 06:34:30 PST 2019\n",
"------------\n",
"\n",
"Distributor ID:\tUbuntu\n",
"Description:\tUbuntu 16.04.5 LTS\n",
"Release:\t16.04\n",
"Codename:\txenial\n",
"\n",
"------------\n",
"HOSTNAME: \n",
"swoose\n",
"\n",
"------------\n",
"Computer Specs:\n",
"\n",
"Architecture: x86_64\n",
"CPU op-mode(s): 32-bit, 64-bit\n",
"Byte Order: Little Endian\n",
"CPU(s): 24\n",
"On-line CPU(s) list: 0-23\n",
"Thread(s) per core: 2\n",
"Core(s) per socket: 6\n",
"Socket(s): 2\n",
"NUMA node(s): 1\n",
"Vendor ID: GenuineIntel\n",
"CPU family: 6\n",
"Model: 44\n",
"Model name: Intel(R) Xeon(R) CPU X5670 @ 2.93GHz\n",
"Stepping: 2\n",
"CPU MHz: 2925.866\n",
"BogoMIPS: 5851.93\n",
"Virtualization: VT-x\n",
"L1d cache: 32K\n",
"L1i cache: 32K\n",
"L2 cache: 256K\n",
"L3 cache: 12288K\n",
"NUMA node0 CPU(s): 0-23\n",
"Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb kaiser tpr_shadow vnmi flexpriority ept vpid dtherm ida arat\n",
"\n",
"------------\n",
"\n",
"Memory Specs\n",
"\n",
" total used free shared buff/cache available\n",
"Mem: 70G 7.9G 1.2G 1.2G 61G 61G\n",
"Swap: 4.7G 35M 4.6G\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"No LSB modules are available.\n"
]
}
],
"source": [
"%%bash\n",
"echo \"TODAY'S DATE:\"\n",
"date\n",
"echo \"------------\"\n",
"echo \"\"\n",
"#Display operating system info\n",
"lsb_release -a\n",
"echo \"\"\n",
"echo \"------------\"\n",
"echo \"HOSTNAME: \"; hostname \n",
"echo \"\"\n",
"echo \"------------\"\n",
"echo \"Computer Specs:\"\n",
"echo \"\"\n",
"lscpu\n",
"echo \"\"\n",
"echo \"------------\"\n",
"echo \"\"\n",
"echo \"Memory Specs\"\n",
"echo \"\"\n",
"free -mh"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Make directories"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"mkdir: cannot create directory ‘/home/sam/data/virginica’: File exists\n",
"mkdir: cannot create directory ‘/home/sam/analyses/20190103_Cvirginica_vcf_splitting’: File exists\n"
]
}
],
"source": [
"%%bash\n",
"mkdir /home/sam/data/virginica\n",
"mkdir /home/sam/analyses/20190103_Cvirginica_vcf_splitting"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Create variables"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"env: vcf_dir=/home/sam/data/virginica\n",
"env: wd=/home/sam/analyses/20190103_Cvirginica_vcf_splitting\n",
"env: bcftools=/home/sam/software/bcftools-1.9-62-g1ce0f47/bcftools\n",
"env: bgzip=/home/sam/software/bin/bgzip\n",
"env: tabix=/home/sam/software/bin/tabix\n"
]
}
],
"source": [
"%env vcf_dir=/home/sam/data/virginica\n",
"%env wd=/home/sam/analyses/20190103_Cvirginica_vcf_splitting\n",
"%env bcftools=/home/sam/software/bcftools-1.9-62-g1ce0f47/bcftools\n",
"%env bgzip=/home/sam/software/bin/bgzip\n",
"%env tabix=/home/sam/software/bin/tabix"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Check software versions"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"bcftools 1.9-62-g1ce0f47\n",
"Using htslib 1.9-44-g80f3557\n",
"Copyright (C) 2018 Genome Research Ltd.\n",
"License Expat: The MIT/Expat license\n",
"This is free software: you are free to change and redistribute it.\n",
"There is NO WARRANTY, to the extent permitted by law.\n",
"bgzip (htslib) 1.9-44-g80f3557\n",
"Copyright (C) 2018 Genome Research Ltd.\n",
"tabix (htslib) 1.9-44-g80f3557\n",
"Copyright (C) 2018 Genome Research Ltd.\n"
]
}
],
"source": [
"%%bash\n",
"${bcftools} --version\n",
"${bgzip} --version\n",
"${tabix} --version"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Download VCF file"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"receiving incremental file list\n",
"total 0\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"ERROR: module is write only\n",
"rsync error: syntax or usage error (code 1) at main.c(782) [sender=3.0.9]\n",
"rsync: connection unexpectedly closed (110 bytes received so far) [Receiver]\n",
"rsync error: error in rsync protocol data stream (code 12) at io.c(226) [Receiver=3.1.1]\n"
]
}
],
"source": [
"%%bash\n",
"cd ${vcf_dir}\n",
"\n",
"rsync \\\n",
"--archive \\\n",
"--verbose \\\n",
"--progress \\\n",
"gannet:/volume1/seashell/eog_v2/VCF_files/Combined.SNP.TRSdp5g95FnDNAmaf05.vcf.gz .\n",
"\n",
"# Uncomment line below to download via web\n",
"# wget http://gannet.fish.washington.edu/seashell/eog_v2/VCF_files/Combined.SNP.TRSdp5g95FnDNAmaf05.vcf.gz\n",
"\n",
"ls -lh"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"receiving incremental file list\n",
"Combined.SNP.TRSdp5g95FnDNAmaf05.vcf.gz\n",
"\r",
" 0 0% 0.00kB/s 0:00:00 \r",
" 84,574,208 0% 80.66MB/s 0:06:34 \r",
" 190,316,544 0% 90.80MB/s 0:05:49 \r",
" 299,958,272 0% 95.42MB/s 0:05:31 \r",
" 391,118,848 1% 93.32MB/s 0:05:37 \r",
" 496,795,648 1% 98.36MB/s 0:05:19 \r",
" 590,086,144 1% 95.38MB/s 0:05:28 \r",
" 676,659,200 2% 89.88MB/s 0:05:47 \r",
" 793,935,872 2% 96.11MB/s 0:05:23 \r",
" 904,429,568 2% 97.26MB/s 0:05:18 \r",
" 1,006,174,208 3% 99.28MB/s 0:05:11 \r",
" 1,114,243,072 3% 104.41MB/s 0:04:54 \r",
" 1,220,050,944 3% 101.67MB/s 0:05:01 \r",
" 1,337,360,384 4% 103.30MB/s 0:04:55 \r",
" 1,441,398,784 4% 103.84MB/s 0:04:53 \r",
" 1,522,892,800 4% 97.50MB/s 0:05:11 \r",
" 1,606,909,952 4% 92.30MB/s 0:05:28 \r",
" 1,718,157,312 5% 90.86MB/s 0:05:32 \r",
" 1,834,909,696 5% 93.89MB/s 0:05:20 \r",
" 1,949,040,640 5% 101.68MB/s 0:04:54 \r",
" 2,019,000,320 6% 98.05MB/s 0:05:05 \r",
" 2,091,679,744 6% 88.88MB/s 0:05:35 \r",
" 2,191,818,752 6% 84.92MB/s 0:05:50 \r",
" 2,296,512,512 7% 82.68MB/s 0:05:58 \r",
" 2,413,297,664 7% 94.08MB/s 0:05:13 \r",
" 2,522,316,800 7% 101.88MB/s 0:04:48 \r",
" 2,609,053,696 7% 98.74MB/s 0:04:57 \r",
" 2,709,422,080 8% 97.71MB/s 0:04:59 \r",
" 2,812,739,584 8% 94.53MB/s 0:05:08 \r",
" 2,930,081,792 8% 97.29MB/s 0:04:58 \r",
" 3,040,772,096 9% 103.01MB/s 0:04:40 \r",
" 3,147,563,008 9% 104.54MB/s 0:04:35 \r",
" 3,235,381,248 9% 100.84MB/s 0:04:44 \r",
" 3,335,258,112 10% 96.67MB/s 0:04:56 \r",
" 3,452,534,784 10% 98.25MB/s 0:04:50 \r",
" 3,552,051,200 10% 95.39MB/s 0:04:57 \r",
" 3,631,480,832 11% 93.41MB/s 0:05:03 \r",
" 3,733,028,864 11% 93.80MB/s 0:05:01 \r",
" 3,827,728,384 11% 88.48MB/s 0:05:18 \r",
" 3,922,395,136 12% 88.36MB/s 0:05:17 \r",
" 4,035,903,488 12% 96.49MB/s 0:04:49 \r",
" 4,139,089,920 12% 96.89MB/s 0:04:47 \r",
" 4,256,399,360 13% 102.28MB/s 0:04:31 \r",
" 4,349,558,784 13% 101.92MB/s 0:04:31 \r",
" 4,396,810,240 13% 86.11MB/s 0:05:20 \r",
" 4,500,488,192 13% 86.23MB/s 0:05:18 \r",
" 4,585,160,704 14% 78.44MB/s 0:05:49 \r",
" 4,685,529,088 14% 80.16MB/s 0:05:40 \r",
" 4,779,671,552 14% 91.35MB/s 0:04:57 \r",
" 4,872,241,152 14% 88.70MB/s 0:05:05 \r",
" 4,966,940,672 15% 91.07MB/s 0:04:56 \r",
" 5,084,250,112 15% 95.11MB/s 0:04:42 \r",
" 5,200,969,728 15% 100.52MB/s 0:04:26 \r",
" 5,310,349,312 16% 104.53MB/s 0:04:15 \r",
" 5,403,934,720 16% 104.27MB/s 0:04:15 \r",
" 5,494,702,080 16% 97.93MB/s 0:04:30 \r",
" 5,572,329,472 17% 88.61MB/s 0:04:58 \r",
" 5,689,638,912 17% 90.50MB/s 0:04:50 \r",
" 5,803,474,944 17% 95.33MB/s 0:04:34 \r",
" 5,920,784,384 18% 101.66MB/s 0:04:16 \r",
" 6,028,361,728 18% 108.81MB/s 0:03:58 \r",
" 6,100,058,112 18% 95.02MB/s 0:04:32 \r",
" 6,143,934,464 18% 78.83MB/s 0:05:28 \r",
" 6,234,275,840 19% 72.58MB/s 0:05:55 \r",
" 6,325,239,808 19% 68.74MB/s 0:06:13 \r",
" 6,440,157,184 19% 81.15MB/s 0:05:15 \r",
" 6,546,751,488 20% 95.99MB/s 0:04:25 \r",
" 6,650,429,440 20% 99.17MB/s 0:04:15 \r",
" 6,767,149,056 20% 105.31MB/s 0:03:59 \r",
" 6,883,868,672 21% 105.71MB/s 0:03:57 \r",
" 6,969,786,368 21% 100.94MB/s 0:04:08 \r",
" 7,037,779,968 21% 92.01MB/s 0:04:31 \r",
" 7,155,449,856 21% 92.23MB/s 0:04:29 \r",
" 7,223,181,312 22% 80.62MB/s 0:05:07 \r",
" 7,338,917,888 22% 87.70MB/s 0:04:41 \r",
" 7,430,242,304 22% 93.64MB/s 0:04:22 \r",
" 7,513,309,184 23% 85.38MB/s 0:04:47 \r",
" 7,620,526,080 23% 94.81MB/s 0:04:17 \r",
" 7,734,886,400 23% 94.48MB/s 0:04:17 \r",
" 7,847,739,392 24% 99.61MB/s 0:04:03 \r",
" 7,948,566,528 24% 103.85MB/s 0:03:52 \r",
" 8,028,258,304 24% 97.26MB/s 0:04:07 \r",
" 8,123,809,792 24% 92.73MB/s 0:04:18 \r",
" 8,240,889,856 25% 93.73MB/s 0:04:14 \r",
" 8,357,609,472 25% 97.52MB/s 0:04:03 \r",
" 8,456,765,440 25% 94.90MB/s 0:04:08 \r",
" 8,542,191,616 26% 92.73MB/s 0:04:13 \r",
" 8,626,470,912 26% 85.46MB/s 0:04:34 \r",
" 8,736,342,016 26% 83.94MB/s 0:04:38 \r",
" 8,850,833,408 27% 94.02MB/s 0:04:07 \r",
" 8,958,476,288 27% 99.32MB/s 0:03:52 \r",
" 9,053,863,936 27% 101.97MB/s 0:03:45 \r",
" 9,169,928,192 28% 103.45MB/s 0:03:41 \r",
" 9,287,237,632 28% 104.12MB/s 0:03:39 \r",
" 9,381,052,416 28% 100.83MB/s 0:03:45 \r",
" 9,470,738,432 29% 99.47MB/s 0:03:47 \r",
" 9,582,116,864 29% 98.35MB/s 0:03:49 \r",
" 9,697,198,080 29% 97.82MB/s 0:03:49 \r",
" 9,805,987,840 30% 101.39MB/s 0:03:39 \r",
" 9,916,973,056 30% 106.47MB/s 0:03:28 \r",
" 10,003,742,720 30% 100.60MB/s 0:03:39 \r",
" 10,087,825,408 30% 93.20MB/s 0:03:56 \r",
" 10,186,194,944 31% 90.72MB/s 0:04:01 \r",
" 10,300,850,176 31% 91.59MB/s 0:03:58 \r",
" 10,344,464,384 31% 80.97MB/s 0:04:28 \r",
" 10,457,776,128 32% 87.92MB/s 0:04:06 \r",
" 10,514,595,840 32% 73.09MB/s 0:04:55 \r",
" 10,591,535,104 32% 64.70MB/s 0:05:32 \r",
" 10,708,320,256 32% 81.30MB/s 0:04:23 \r",
" 10,823,991,296 33% 81.83MB/s 0:04:20 \r",
" 10,886,381,568 33% 88.71MB/s 0:03:59 \r",
" 10,980,163,584 33% 92.73MB/s 0:03:48 \r",
" 11,073,978,368 33% 87.25MB/s 0:04:01 \r",
" 11,184,537,600 34% 86.03MB/s 0:04:03 \r",
" 11,277,697,024 34% 86.97MB/s 0:03:59 \r",
" 11,391,205,376 34% 91.35MB/s 0:03:47 \r",
" 11,485,741,056 35% 91.51MB/s 0:03:45 \r",
" 11,565,531,136 35% 78.46MB/s 0:04:22 \r",
" 11,682,742,272 35% 89.09MB/s 0:03:49 \r",
" 11,798,478,848 36% 89.58MB/s 0:03:47 \r",
" 11,912,937,472 36% 93.96MB/s 0:03:35 \r",
" 11,974,246,400 36% 97.52MB/s 0:03:27 \r",
" 12,061,605,888 36% 90.40MB/s 0:03:42 \r",
" 12,118,196,224 37% 76.28MB/s 0:04:22 \r",
" 12,231,016,448 37% 75.89MB/s 0:04:22 \r",
" 12,347,703,296 37% 89.11MB/s 0:03:42 \r",
" 12,463,538,176 38% 95.90MB/s 0:03:25 \r",
" 12,572,262,400 38% 108.34MB/s 0:03:00 \r",
" 12,658,966,528 38% 102.11MB/s 0:03:11 \r",
" 12,717,719,552 38% 88.28MB/s 0:03:40 \r",
" 12,829,753,344 39% 87.38MB/s 0:03:41 \r",
" 12,930,940,928 39% 85.58MB/s 0:03:44 \r",
" 13,033,963,520 39% 89.47MB/s 0:03:34 \r",
" 13,145,571,328 40% 102.08MB/s 0:03:06 \r",
" 13,255,049,216 40% 101.47MB/s 0:03:06 \r",
" 13,364,396,032 40% 103.42MB/s 0:03:02 \r",
" 13,420,199,936 41% 88.46MB/s 0:03:32 \r",
" 13,520,306,176 41% 85.82MB/s 0:03:37 \r",
" 13,637,648,384 41% 87.63MB/s 0:03:31 \r",
" 13,754,302,464 42% 89.32MB/s 0:03:26 \r",
" 13,862,567,936 42% 105.55MB/s 0:02:53 \r",
" 13,932,167,168 42% 91.54MB/s 0:03:19 \r",
" 14,035,681,280 42% 88.46MB/s 0:03:25 \r",
" 14,152,990,720 43% 88.61MB/s 0:03:23 \r",
" 14,217,052,160 43% 78.78MB/s 0:03:48 \r",
" 14,334,296,064 43% 95.95MB/s 0:03:06 \r",
" 14,379,614,208 44% 81.51MB/s 0:03:38 \r",
" 14,467,497,984 44% 74.54MB/s 0:03:58 \r",
" 14,584,807,424 44% 87.16MB/s 0:03:22 \r",
" 14,701,461,504 45% 87.02MB/s 0:03:21 \r",
" 14,818,803,712 45% 104.79MB/s 0:02:46 \r",
" 14,883,323,904 45% 99.22MB/s 0:02:54 \r",
" 14,965,014,528 45% 83.37MB/s 0:03:27 \r",
" 15,039,725,568 46% 72.94MB/s 0:03:55 \r",
" 15,113,388,032 46% 61.51MB/s 0:04:38 \r",
" 15,216,279,552 46% 69.51MB/s 0:04:04 \r",
" 15,288,500,224 46% 68.28MB/s 0:04:08 \r",
" 15,392,014,336 47% 75.60MB/s 0:03:42 \r",
" 15,509,225,472 47% 87.79MB/s 0:03:10 \r",
" 15,574,892,544 47% 79.55MB/s 0:03:29 \r",
" 15,671,459,840 48% 91.30MB/s 0:03:01 \r",
" 15,762,489,344 48% 88.33MB/s 0:03:06 \r",
" 15,817,900,032 48% 73.59MB/s 0:03:43 \r",
" 15,929,966,592 48% 84.66MB/s 0:03:12 \r",
" 16,047,276,032 49% 89.67MB/s 0:03:00 \r",
" 16,128,638,976 49% 86.91MB/s 0:03:05 \r",
" 16,189,161,472 49% 88.12MB/s 0:03:02 \r",
" 16,244,375,552 49% 74.63MB/s 0:03:34 \r",
" 16,340,582,400 50% 69.62MB/s 0:03:48 \r",
" 16,457,891,840 50% 78.56MB/s 0:03:21 \r",
" 16,550,166,528 50% 84.80MB/s 0:03:05 \r",
" 16,657,547,264 51% 97.05MB/s 0:02:40 \r",
" 16,770,564,096 51% 101.00MB/s 0:02:33 \r",
" 16,851,402,752 51% 87.64MB/s 0:02:55 \r",
" 16,970,121,216 51% 94.95MB/s 0:02:41 \r",
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" 17,175,674,880 52% 84.91MB/s 0:02:57 \r",
" 17,237,016,576 52% 83.64MB/s 0:02:59 \r",
" 17,277,124,608 52% 63.77MB/s 0:03:55 \r",
" 17,371,463,680 53% 59.78MB/s 0:04:09 \r",
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" 17,569,873,920 53% 75.60MB/s 0:03:14 \r",
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" 17,756,487,680 54% 91.68MB/s 0:02:38 \r",
" 17,808,064,512 54% 83.47MB/s 0:02:53 \r",
" 17,881,497,600 54% 74.35MB/s 0:03:13 \r",
" 17,996,808,192 55% 80.06MB/s 0:02:58 \r",
" 18,108,022,784 55% 83.88MB/s 0:02:49 \r",
" 18,195,415,040 55% 92.40MB/s 0:02:32 \r",
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" 19,002,916,864 58% 74.47MB/s 0:02:58 \r",
" 19,118,292,992 58% 76.44MB/s 0:02:52 \r",
" 19,230,326,784 58% 92.80MB/s 0:02:21 \r",
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" 19,409,502,208 59% 97.01MB/s 0:02:13 \r",
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" 19,620,331,520 60% 93.05MB/s 0:02:16 \r",
" 19,650,215,936 60% 81.30MB/s 0:02:36 \r",
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" 19,793,444,864 60% 63.67MB/s 0:03:17 \r",
" 19,877,068,800 60% 54.53MB/s 0:03:48 \r",
" 19,978,256,384 61% 63.64MB/s 0:03:14 \r",
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" 20,215,169,024 61% 66.40MB/s 0:03:02 \r",
" 20,268,810,240 62% 62.55MB/s 0:03:13 \r",
" 20,335,525,888 62% 62.32MB/s 0:03:12 \r",
" 20,382,220,288 62% 50.41MB/s 0:03:57 \r",
" 20,454,834,176 62% 55.58MB/s 0:03:34 \r",
" 20,528,234,496 62% 57.47MB/s 0:03:25 \r",
" 20,591,378,432 63% 56.69MB/s 0:03:27 \r",
" 20,651,442,176 63% 60.77MB/s 0:03:12 \r",
" 20,684,472,320 63% 48.27MB/s 0:04:01 \r",
" 20,709,572,608 63% 39.81MB/s 0:04:52 \r",
" 20,770,684,928 63% 39.36MB/s 0:04:54 \r",
" 20,839,661,568 63% 41.33MB/s 0:04:38 \r",
" 20,900,446,208 64% 51.53MB/s 0:03:42 \r",
" 20,953,956,352 64% 51.81MB/s 0:03:40 \r",
" 21,001,404,416 64% 48.92MB/s 0:03:52 \r",
" 21,081,686,016 64% 51.31MB/s 0:03:40 \r",
" 21,153,153,024 64% 53.58MB/s 0:03:29 \r",
" 21,225,275,392 65% 63.14MB/s 0:02:56 \r",
" 21,319,385,088 65% 69.73MB/s 0:02:38 \r",
" 21,394,096,128 65% 65.22MB/s 0:02:48 \r",
" 21,470,380,032 65% 64.20MB/s 0:02:49 \r",
" 21,545,615,360 65% 63.94MB/s 0:02:49 \r",
" 21,631,860,736 66% 63.47MB/s 0:02:49 \r",
" 21,712,338,944 66% 59.16MB/s 0:03:00 \r",
" 21,754,183,680 66% 54.26MB/s 0:03:16 \r",
" 21,828,993,024 66% 55.63MB/s 0:03:09 \r",
" 21,947,744,256 67% 64.23MB/s 0:02:42 \r",
" 22,065,053,696 67% 83.36MB/s 0:02:03 \r",
" 22,182,395,904 67% 101.21MB/s 0:01:40 \r",
" 22,283,223,040 68% 108.38MB/s 0:01:33 \r",
" 22,363,471,872 68% 99.19MB/s 0:01:41 \r",
" 22,469,181,440 68% 96.42MB/s 0:01:43 \r",
" 22,576,103,424 69% 93.94MB/s 0:01:44 \r",
" 22,671,425,536 69% 92.62MB/s 0:01:45 \r",
" 22,788,734,976 69% 101.47MB/s 0:01:34 \r",
" 22,882,091,008 70% 98.52MB/s 0:01:36 \r",
" 22,974,267,392 70% 95.00MB/s 0:01:39 \r",
" 23,075,291,136 70% 96.36MB/s 0:01:36 \r",
" 23,183,458,304 71% 93.41MB/s 0:01:38 \r",
" 23,298,179,072 71% 98.46MB/s 0:01:32 \r",
" 23,400,644,608 71% 100.90MB/s 0:01:29 \r",
" 23,503,896,576 71% 101.43MB/s 0:01:28 \r",
" 23,602,298,880 72% 99.93MB/s 0:01:28 \r",
" 23,700,045,824 72% 95.88MB/s 0:01:31 \r",
" 23,815,487,488 72% 98.98MB/s 0:01:27 \r",
" 23,921,065,984 73% 99.54MB/s 0:01:25 \r",
" 24,038,408,192 73% 104.05MB/s 0:01:20 \r",
" 24,145,166,336 73% 106.20MB/s 0:01:18 \r",
" 24,236,130,304 74% 100.36MB/s 0:01:21 \r",
" 24,334,401,536 74% 98.62MB/s 0:01:22 \r",
" 24,427,233,280 74% 92.77MB/s 0:01:26 \r",
" 24,537,038,848 75% 93.50MB/s 0:01:24 \r",
" 24,650,940,416 75% 98.97MB/s 0:01:18 \r",
" 24,740,954,112 75% 97.00MB/s 0:01:19 \r",
" 24,832,901,120 76% 96.79MB/s 0:01:18 \r",
" 24,944,476,160 76% 97.21MB/s 0:01:17 \r",
" 25,012,764,672 76% 86.33MB/s 0:01:26 \r",
" 25,081,380,864 76% 81.22MB/s 0:01:30 \r",
" 25,149,636,608 77% 75.57MB/s 0:01:36 \r",
" 25,214,582,784 77% 62.89MB/s 0:01:55 \r",
" 25,300,303,872 77% 63.92MB/s 0:01:52 \r",
" 25,389,432,832 77% 65.17MB/s 0:01:48 \r",
" 25,481,445,376 78% 67.53MB/s 0:01:43 \r",
" 25,557,729,280 78% 68.48MB/s 0:01:41 \r",
" 25,628,770,304 78% 65.22MB/s 0:01:45 \r",
" 25,715,277,824 78% 65.84MB/s 0:01:42 \r",
" 25,808,863,232 79% 65.60MB/s 0:01:41 \r",
" 25,887,244,288 79% 62.30MB/s 0:01:45 \r",
" 25,923,780,608 79% 58.27MB/s 0:01:52 \r",
" 25,982,664,704 79% 54.35MB/s 0:01:59 \r",
" 26,053,902,336 79% 52.22MB/s 0:02:03 \r",
" 26,142,310,400 80% 58.63MB/s 0:01:48 \r",
" 26,234,585,088 80% 68.26MB/s 0:01:31 \r",
" 26,304,053,248 80% 68.71MB/s 0:01:30 \r",
" 26,388,987,904 80% 66.52MB/s 0:01:31 \r",
" 26,458,980,352 81% 62.77MB/s 0:01:36 \r",
" 26,556,497,920 81% 62.95MB/s 0:01:34 \r",
" 26,624,917,504 81% 61.89MB/s 0:01:35 \r",
" 26,689,929,216 81% 55.56MB/s 0:01:44 \r",
" 26,755,301,376 81% 56.45MB/s 0:01:41 \r",
" 26,813,071,360 82% 51.53MB/s 0:01:50 \r",
" 26,886,537,216 82% 53.71MB/s 0:01:44 \r",
" 26,967,801,856 82% 62.31MB/s 0:01:28 \r",
" 27,079,049,216 82% 72.60MB/s 0:01:14 \r",
" 27,149,697,024 83% 75.48MB/s 0:01:11 \r",
" 27,221,295,104 83% 76.56MB/s 0:01:09 \r",
" 27,290,501,120 83% 76.94MB/s 0:01:07 \r",
" 27,362,328,576 83% 64.45MB/s 0:01:20 \r",
" 27,438,612,480 84% 62.59MB/s 0:01:21 \r",
" 27,536,654,336 84% 64.51MB/s 0:01:17 \r",
" 27,610,578,944 84% 65.02MB/s 0:01:15 \r",
" 27,677,163,520 84% 63.84MB/s 0:01:16 \r",
" 27,767,341,056 85% 66.18MB/s 0:01:11 \r",
" 27,846,246,400 85% 62.57MB/s 0:01:14 \r",
" 27,930,656,768 85% 63.22MB/s 0:01:12 \r",
" 28,007,202,816 85% 65.08MB/s 0:01:09 \r",
" 28,099,215,360 86% 66.24MB/s 0:01:07 \r",
" 28,195,160,064 86% 65.37MB/s 0:01:06 \r",
" 28,244,705,280 86% 58.95MB/s 0:01:12 \r",
" 28,324,331,520 86% 62.08MB/s 0:01:07 \r",
" 28,416,114,688 87% 64.48MB/s 0:01:04 \r",
" 28,511,141,888 87% 72.95MB/s 0:00:55 \r",
" 28,621,897,728 87% 90.00MB/s 0:00:43 \r",
" 28,730,687,488 88% 96.96MB/s 0:00:39 \r",
" 28,780,756,992 88% 86.96MB/s 0:00:43 \r",
" 28,833,644,544 88% 76.91MB/s 0:00:48 \r",
" 28,885,778,432 88% 62.93MB/s 0:00:58 \r",
" 28,944,138,240 88% 50.90MB/s 0:01:11 \r",
" 29,022,224,384 88% 55.33MB/s 0:01:03 \r",
" 29,108,994,048 89% 59.06MB/s 0:00:58 \r",
" 29,201,268,736 89% 64.86MB/s 0:00:51 \r",
" 29,290,397,696 89% 68.70MB/s 0:00:47 \r",
" 29,370,875,904 89% 68.64MB/s 0:00:46 \r",
" 29,435,101,184 90% 64.98MB/s 0:00:48 \r",
" 29,477,044,224 90% 56.72MB/s 0:00:54 \r",
" 29,565,124,608 90% 56.10MB/s 0:00:53 \r",
" 29,641,408,512 90% 51.52MB/s 0:00:56 \r",
" 29,705,764,864 90% 53.97MB/s 0:00:53 \r",
" 29,766,483,968 91% 58.25MB/s 0:00:48 \r",
" 29,848,240,128 91% 57.53MB/s 0:00:47 \r",
" 29,944,283,136 91% 69.58MB/s 0:00:37 \r",
" 30,035,935,232 92% 70.43MB/s 0:00:36 \r",
" 30,128,046,080 92% 77.12MB/s 0:00:31 \r",
" 30,198,562,816 92% 77.41MB/s 0:00:30 \r",
" 30,271,438,848 92% 72.29MB/s 0:00:32 \r",
" 30,337,892,352 92% 72.05MB/s 0:00:31 \r",
" 30,398,218,240 93% 63.87MB/s 0:00:34 \r",
" 30,485,020,672 93% 67.72MB/s 0:00:31 \r",
" 30,578,049,024 93% 72.49MB/s 0:00:27 \r",
" 30,694,866,944 94% 84.39MB/s 0:00:22 \r",
" 30,812,176,384 94% 98.77MB/s 0:00:18 \r",
" 30,921,392,128 94% 104.12MB/s 0:00:16 \r",
" 31,010,062,336 94% 103.08MB/s 0:00:15 \r",
" 31,115,673,600 95% 100.40MB/s 0:00:14 \r",
" 31,210,340,352 95% 95.00MB/s 0:00:14 \r",
" 31,297,110,016 95% 89.65MB/s 0:00:14 \r",
" 31,400,394,752 96% 93.13MB/s 0:00:13 \r",
" 31,496,306,688 96% 90.82MB/s 0:00:12 \r",
" 31,608,733,696 96% 95.06MB/s 0:00:10 \r",
" 31,723,978,752 97% 101.85MB/s 0:00:08 \r",
" 31,813,238,784 97% 97.99MB/s 0:00:08 \r",
" 31,903,809,536 97% 96.72MB/s 0:00:07 \r",
" 31,984,320,512 97% 89.15MB/s 0:00:07 \r",
" 32,086,917,120 98% 86.14MB/s 0:00:06 \r",
" 32,197,410,816 98% 91.66MB/s 0:00:04 \r",
" 32,288,604,160 98% 91.81MB/s 0:00:03 \r",
" 32,384,647,168 99% 95.52MB/s 0:00:02 \r",
" 32,460,472,320 99% 89.13MB/s 0:00:02 \r",
" 32,576,897,024 99% 90.54MB/s 0:00:00 \r",
" 32,645,951,849 100% 82.68MB/s 0:06:16 (xfr#1, to-chk=0/1)\n",
"\n",
"sent 30 bytes received 32,649,937,077 bytes 86,489,899.62 bytes/sec\n",
"total size is 32,645,951,849 speedup is 1.00\n",
"total 31G\n",
"-rwxrwxrwx 1 sam users 31G Dec 19 22:03 Combined.SNP.TRSdp5g95FnDNAmaf05.vcf.gz\n"
]
}
],
"source": [
"%%bash\n",
"cd ${vcf_dir}\n",
"\n",
"rsync \\\n",
"--archive \\\n",
"--verbose \\\n",
"--progress \\\n",
"gannet:/volume1/web/seashell/eog_v2/VCF_files/Combined.SNP.TRSdp5g95FnDNAmaf05.vcf.gz .\n",
"\n",
"# Uncomment line below to download via web\n",
"# wget http://gannet.fish.washington.edu/seashell/eog_v2/VCF_files/Combined.SNP.TRSdp5g95FnDNAmaf05.vcf.gz\n",
"\n",
"ls -lh"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Unzip VCF"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"total 186G\n",
"-rwxrwxrwx 1 sam users 186G Dec 19 22:03 Combined.SNP.TRSdp5g95FnDNAmaf05.vcf\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n",
"real\t49m37.000s\n",
"user\t20m21.120s\n",
"sys\t2m30.532s\n"
]
}
],
"source": [
"%%bash\n",
"cd ${vcf_dir}\n",
"\n",
"time \\\n",
"gunzip Combined.SNP.TRSdp5g95FnDNAmaf05.vcf.gz\n",
"\n",
"ls -lh"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Sort and bgzip"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"awk: cannot open Combined.SNP.TRSdp5g95FnDNAmaf05.vcf (No such file or directory)\n",
"\n",
"real\t0m0.098s\n",
"user\t0m0.004s\n",
"sys\t0m0.000s\n"
]
}
],
"source": [
"%%bash\n",
"time \\\n",
"awk '$1 ~ /^#/ {print $0;next} {print $0 | \"sort -k1,1 -k2,2n\"}' Combined.SNP.TRSdp5g95FnDNAmaf05.vcf |\\\n",
"${bgzip} \\\n",
"--threads 18 \\\n",
"> ${wd}/Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"sort: write failed: /tmp/sortDMZSYb: No space left on device\n",
"\n",
"real\t26m25.034s\n",
"user\t3m37.928s\n",
"sys\t1m59.788s\n"
]
}
],
"source": [
"%%bash\n",
"cd ${vcf_dir}\n",
"\n",
"time \\\n",
"awk '$1 ~ /^#/ {print $0;next} {print $0 | \"sort -k1,1 -k2,2n\"}' Combined.SNP.TRSdp5g95FnDNAmaf05.vcf |\\\n",
"${bgzip} \\\n",
"--threads 18 \\\n",
"> ${wd}/Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"No space??"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Filesystem Size Used Avail Use% Mounted on\n",
"udev 36G 0 36G 0% /dev\n",
"tmpfs 7.1G 722M 6.4G 10% /run\n",
"/dev/sda6 224G 80G 133G 38% /\n",
"tmpfs 36G 221M 36G 1% /dev/shm\n",
"tmpfs 5.0M 4.0K 5.0M 1% /run/lock\n",
"tmpfs 36G 0 36G 0% /sys/fs/cgroup\n",
"/dev/sdb1 917G 508G 363G 59% /home\n",
"cgmfs 100K 0 100K 0% /run/cgmanager/fs\n",
"tmpfs 7.1G 168K 7.1G 1% /run/user/1000\n",
"//owl.fish.washington.edu/web 51T 48T 2.8T 95% /mnt/owl\n"
]
}
],
"source": [
"%%bash\n",
"df -h"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Deleted some stuff..."
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Filesystem Size Used Avail Use% Mounted on\n",
"udev 36G 0 36G 0% /dev\n",
"tmpfs 7.1G 722M 6.4G 10% /run\n",
"/dev/sda6 224G 80G 133G 38% /\n",
"tmpfs 36G 250M 36G 1% /dev/shm\n",
"tmpfs 5.0M 4.0K 5.0M 1% /run/lock\n",
"tmpfs 36G 0 36G 0% /sys/fs/cgroup\n",
"/dev/sdb1 917G 212G 659G 25% /home\n",
"cgmfs 100K 0 100K 0% /run/cgmanager/fs\n",
"tmpfs 7.1G 168K 7.1G 1% /run/user/1000\n",
"//owl.fish.washington.edu/web 51T 48T 2.8T 95% /mnt/owl\n"
]
}
],
"source": [
"%%bash\n",
"df -h"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"sort: write failed: /tmp/sortrHTYQb: No space left on device\n",
"\n",
"real\t30m51.276s\n",
"user\t3m39.152s\n",
"sys\t1m58.672s\n"
]
}
],
"source": [
"%%bash\n",
"cd ${vcf_dir}\n",
"\n",
"time \\\n",
"awk '$1 ~ /^#/ {print $0;next} {print $0 | \"sort -k1,1 -k2,2n\"}' Combined.SNP.TRSdp5g95FnDNAmaf05.vcf |\\\n",
"${bgzip} \\\n",
"--threads 18 \\\n",
"> ${wd}/Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Ran out of space - again. Duh. Just realized the space limitation was in ```/tmp```. Deleting the other files I previously removed had no effect.\n",
"\n",
"Need to fix this..."
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n",
"real\t306m21.798s\n",
"user\t118m7.088s\n",
"sys\t30m32.388s\n"
]
}
],
"source": [
"%%bash\n",
"cd ${vcf_dir}\n",
"\n",
"time \\\n",
"awk '$1 ~ /^#/ {print $0;next} {print $0 | \"sort --temporary-directory=/home/sam/Downloads -k1,1 -k2,2n\"}' Combined.SNP.TRSdp5g95FnDNAmaf05.vcf |\\\n",
"${bgzip} \\\n",
"--threads 18 \\\n",
"> ${wd}/Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Index with ```tabix```"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"total 33G\n",
"-rw-rw-r-- 1 sam sam 33G Jan 2 14:43 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 538K Jan 2 15:14 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz.tbi\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n",
"real\t19m46.280s\n",
"user\t18m55.812s\n",
"sys\t0m22.376s\n"
]
}
],
"source": [
"%%bash\n",
"cd ${wd}\n",
"\n",
"time \\\n",
"${tabix} --preset vcf Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz\n",
"\n",
"ls -lh"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Fill AN/AC values"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"total 66G\n",
"-rw-rw-r-- 1 sam sam 33G Jan 2 17:05 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 33G Jan 2 14:43 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 538K Jan 2 15:14 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz.tbi\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n",
"real\t109m50.921s\n",
"user\t210m56.972s\n",
"sys\t1m53.408s\n"
]
}
],
"source": [
"%%bash\n",
"cd ${wd}\n",
"\n",
"export BCFTOOLS_PLUGINS=/home/sam/software/bcftools-1.9-62-g1ce0f47/plugins\n",
"\n",
"time \\\n",
"${bcftools} plugin fill-AN-AC Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz \\\n",
"--output-type z \\\n",
"--threads 18 \\\n",
"--output Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.vcf.gz\n",
"\n",
"ls -lh"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
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"bash: line 5: bcftools: command not found\n",
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"bash: line 5: bcftools: command not found\n",
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"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n"
]
}
],
"source": [
"%%bash\n",
"cd ${wd}\n",
"\n",
"for file in Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.vcf.gz; do\n",
" for sample in $($bcftools query -l $file); do\n",
" bcftools view \\\n",
" --min-ac 1 \\\n",
" --output-type z \\\n",
" --samples $sample \\\n",
" --output-file ${file/.vcf*/.$sample.vcf.gz} \\\n",
" --threads 18 \\\n",
" ${file}\n",
" done\n",
"done"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
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"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n"
]
}
],
"source": [
"%%bash\n",
"cd ${wd}\n",
"\n",
"for file in Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.vcf.gz; do\n",
" for sample in `$bcftools query -l $file`; do\n",
" bcftools view \\\n",
" --min-ac 1 \\\n",
" --output-type z \\\n",
" --samples $sample \\\n",
" --output-file ${file/.vcf*/.$sample.vcf.gz} \\\n",
" --threads 18 \\\n",
" ${file}\n",
" done\n",
"done"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
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"bash: line 5: bcftools: command not found\n",
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"bash: line 5: bcftools: command not found\n",
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"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n",
"bash: line 5: bcftools: command not found\n"
]
}
],
"source": [
"%%bash\n",
"cd ${wd}\n",
"\n",
"for file in Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.vcf.gz; do\n",
" for sample in $(/home/sam/software/bcftools-1.9-62-g1ce0f47/bcftools query -l $file); do\n",
" bcftools view \\\n",
" --min-ac 1 \\\n",
" --output-type z \\\n",
" --samples $sample \\\n",
" --output-file ${file/.vcf*/.$sample.vcf.gz} \\\n",
" --threads 18 \\\n",
" ${file}\n",
" done\n",
"done"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {},
"outputs": [],
"source": [
"%%bash\n",
"cd ${wd}\n",
"\n",
"for file in Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.vcf.gz; do\n",
" for sample in $($bcftools query -l $file); do\n",
" ${bcftools} view \\\n",
" --min-ac 1 \\\n",
" --output-type z \\\n",
" --samples $sample \\\n",
" --output-file ${file/.vcf*/.$sample.vcf.gz} \\\n",
" --threads 18 \\\n",
" ${file}\n",
" done\n",
"done"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n",
"real\t21m56.303s\n",
"user\t14m55.344s\n",
"sys\t4m17.120s\n"
]
}
],
"source": [
"%%bash\n",
"\n",
"# Copy data to Gannet\n",
"cd /home/sam/analyses\n",
"time \\\n",
"rsync \\\n",
"--archive \\\n",
"--relative \\\n",
"./20190103_Cvirginica_vcf_splitting gannet:/volume1/web/Atumefaciens"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"total 113G\n",
"-rw-rw-r-- 1 sam sam 33G Jan 2 14:43 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 538K Jan 2 15:14 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz.tbi\n",
"-rw-rw-r-- 1 sam sam 33G Jan 2 17:05 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 567M Jan 2 20:28 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CL_1.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 586M Jan 2 21:32 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CL_2.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 588M Jan 2 22:36 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CL_3.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 560M Jan 2 23:41 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CL_4.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 549M Jan 3 00:45 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CL_5.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 572M Jan 3 01:50 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CL_6.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 527M Jan 3 02:54 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CLP_1.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 530M Jan 3 03:58 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CLP_2.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 541M Jan 3 05:02 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CLP_3.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 534M Jan 3 06:05 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CLP_4.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 540M Jan 3 07:09 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CLP_5.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 540M Jan 3 08:14 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CLP_6.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 531M Jan 3 09:17 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CS_1.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 527M Jan 3 10:21 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CS_2.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 502M Jan 3 11:25 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CS_3.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 528M Jan 3 12:30 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CS_5.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 524M Jan 3 13:35 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CS_6.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 530M Jan 3 14:38 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CS_7.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 552M Jan 3 15:42 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.DEBY_1.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 568M Jan 3 16:47 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.DEBY_2.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 557M Jan 3 17:50 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.DEBY_3.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 524M Jan 3 18:54 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.DEBY_4.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 562M Jan 3 19:58 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.DEBY_5.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 545M Jan 3 21:02 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.DEBY_6.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 530M Jan 3 22:07 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_1.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 522M Jan 3 23:10 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_3.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 532M Jan 4 00:14 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_4.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 535M Jan 4 01:19 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_5.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 518M Jan 4 02:22 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_6.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 552M Jan 4 03:26 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_7.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 532M Jan 4 04:29 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_VA_1.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 535M Jan 4 05:33 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_VA_2.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 525M Jan 4 06:36 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_VA_3.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 529M Jan 4 07:41 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_VA_4.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 528M Jan 4 08:45 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_VA_5.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 533M Jan 4 09:48 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_VA_6.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 252M Jan 4 10:52 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HG_HG0F2.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 228M Jan 4 11:56 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HG_HG2F1.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 194M Jan 4 13:00 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HG_HG2M5.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 525M Jan 4 14:04 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HI_1.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 524M Jan 4 15:08 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HI_2.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 530M Jan 4 16:13 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HI_3.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 526M Jan 4 17:16 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HI_4.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 515M Jan 4 18:20 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HI_5.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 519M Jan 4 19:23 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HI_6.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 610M Jan 4 20:28 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LM_1_pool.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 619M Jan 4 21:32 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LM_3.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 637M Jan 4 22:36 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LM_4.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 668M Jan 4 23:42 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LM_7.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 598M Jan 5 00:47 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LM_8.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 590M Jan 5 01:51 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LOLA_1.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 579M Jan 5 02:56 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LOLA_2.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 577M Jan 5 04:00 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LOLA_3.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 589M Jan 5 05:04 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LOLA_4.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 576M Jan 5 06:07 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LOLA_5.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 576M Jan 5 07:13 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LOLA_6.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 510M Jan 5 08:16 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.NEH_1.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 482M Jan 5 09:20 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.NEH_2.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 498M Jan 5 10:23 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.NEH_3.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 517M Jan 5 11:27 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.NEH_4.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 490M Jan 5 12:31 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.NEH_5.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 501M Jan 5 13:35 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.NEH_6.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 515M Jan 5 14:40 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.NG_NH0H4.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 450M Jan 5 15:45 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.NG_NH2F6.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 457M Jan 5 16:48 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.NG_NH2F8.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 473M Jan 5 17:51 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.NG_NH2M1.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 585M Jan 5 18:55 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.OBOYS2_1.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 587M Jan 5 19:59 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.OBOYS2_2.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 593M Jan 5 21:03 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.OBOYS2_3.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 572M Jan 5 22:08 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.OBOYS2_4.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 574M Jan 5 23:11 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.OBOYS2_5.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 599M Jan 6 00:16 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.OBOYS2_6.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 584M Jan 6 01:19 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SL_1.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 568M Jan 6 02:23 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SL_2.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 586M Jan 6 03:27 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SL_3.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 572M Jan 6 04:30 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SL_4.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 586M Jan 6 05:34 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SL_5.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 581M Jan 6 06:38 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SL_6.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 528M Jan 6 07:41 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SM_10.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 517M Jan 6 08:45 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SM_11.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 523M Jan 6 09:48 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SM_12.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 531M Jan 6 10:53 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SM_7.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 522M Jan 6 11:56 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SM_8.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 523M Jan 6 12:59 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SM_9.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 514M Jan 6 14:03 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.UMFS_1.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 533M Jan 6 15:07 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.UMFS_2.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 549M Jan 6 16:12 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.UMFS_3.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 548M Jan 6 17:15 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.UMFS_4.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 530M Jan 6 18:19 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.UMFS_5.vcf.gz\n",
"-rw-rw-r-- 1 sam sam 534M Jan 6 19:22 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.UMFS_6.vcf.gz\n"
]
}
],
"source": [
"%%bash\n",
"ls -lhtr ${wd}"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
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"display_name": "Python 3",
"language": "python",
"name": "python3"
},
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