2017-07-18 18:24:57,931 LoggerReporter started INFO: Beginning AnADAMA run with 82 tasks. 2017-07-18 18:24:57,931 LoggerReporter started INFO: Workflow configuration options 2017-07-18 18:24:57,931 LoggerReporter started INFO: strain_profiling_options = --marker_in_clade 0.01 2017-07-18 18:24:57,931 LoggerReporter started INFO: grid_benchmark = off 2017-07-18 18:24:57,931 LoggerReporter started INFO: grid_partition = 2017-07-18 18:24:57,931 LoggerReporter started INFO: pair_identifier = .R1 2017-07-18 18:24:57,931 LoggerReporter started INFO: log_level = INFO 2017-07-18 18:24:57,932 LoggerReporter started INFO: input_extension = fastq.gz 2017-07-18 18:24:57,932 LoggerReporter started INFO: dry_run = False 2017-07-18 18:24:57,932 LoggerReporter started INFO: exclude_target = None 2017-07-18 18:24:57,932 LoggerReporter started INFO: until_task = None 2017-07-18 18:24:57,932 LoggerReporter started INFO: remove_intermediate_output = False 2017-07-18 18:24:57,932 LoggerReporter started INFO: bypass_strain_profiling = False 2017-07-18 18:24:57,932 LoggerReporter started INFO: input = examples/tutorial/input/ 2017-07-18 18:24:57,932 LoggerReporter started INFO: grid_jobs = 0 2017-07-18 18:24:57,932 LoggerReporter started INFO: contaminate_databases = /work/code/biobakery_workflows/examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/ 2017-07-18 18:24:57,932 LoggerReporter started INFO: jobs = 1 2017-07-18 18:24:57,932 LoggerReporter started INFO: grid = None 2017-07-18 18:24:57,932 LoggerReporter started INFO: qc_options = 2017-07-18 18:24:57,932 LoggerReporter started INFO: output = biobakery_workflows_tutorial_output 2017-07-18 18:24:57,932 LoggerReporter started INFO: target = None 2017-07-18 18:24:57,932 LoggerReporter started INFO: grid_environment = None 2017-07-18 18:24:57,932 LoggerReporter started INFO: exclude_task = None 2017-07-18 18:24:57,932 LoggerReporter started INFO: quit_early = False 2017-07-18 18:24:57,932 LoggerReporter started INFO: grid_options = None 2017-07-18 18:24:57,932 LoggerReporter started INFO: threads = 1 2017-07-18 18:24:57,932 LoggerReporter started INFO: skip_nothing = False 2017-07-18 18:24:58,640 LoggerReporter log_event INFO: task 3, kneaddata____CSM5FZ4M : ready and waiting for resources 2017-07-18 18:24:58,641 LoggerReporter log_event INFO: task 3, kneaddata____CSM5FZ4M : starting to run 2017-07-18 18:24:58,792 LoggerReporter task_command INFO: Tracked executable version: kneaddata v0.6.1 2017-07-18 18:24:58,792 LoggerReporter task_command INFO: Executing with shell: kneaddata --input /work/code/biobakery_workflows/examples/tutorial/input/CSM5FZ4M.fastq.gz --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main --threads 1 --output-prefix CSM5FZ4M --reference-db /work/code/biobakery_workflows/examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/ --serial 2017-07-18 18:25:05,428 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Decompressing gzipped file ... Initial number of reads ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/decompressed_CaJZKD_CSM5FZ4M.fastq ): 108134 Running Trimmomatic ... Total reads after trimming ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5FZ4M.trimmed.fastq ): 108064 Decontaminating ... Running bowtie2 ... Running bowtie2 ... Total reads after removing those found in reference database ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5FZ4M_Homo_sapiens_demo_bowtie2_clean.fastq ): 107976 Total reads after merging results from multiple databases ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5FZ4M.fastq ): 107891 Final output file created: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5FZ4M.fastq Stderr: 2017-07-18 18:25:05,429 LoggerReporter log_event INFO: task 3, kneaddata____CSM5FZ4M : completed successfully 2017-07-18 18:25:05,429 LoggerReporter log_event INFO: task 16, metaphlan____CSM5FZ4M : ready and waiting for resources 2017-07-18 18:25:05,429 LoggerReporter log_event INFO: task 16, metaphlan____CSM5FZ4M : starting to run 2017-07-18 18:25:05,527 LoggerReporter task_command INFO: Executing with shell: metaphlan /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5FZ4M.fastq --input_type fastq --output_file /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main/CSM5FZ4M_taxonomic_profile.tsv --samout /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main/CSM5FZ4M_bowtie2.sam --nproc 1 --no_map --tmp_dir /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main 2017-07-18 18:26:02,216 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: 2017-07-18 18:26:02,216 LoggerReporter log_event INFO: task 16, metaphlan____CSM5FZ4M : completed successfully 2017-07-18 18:28:24,130 LoggerReporter log_event INFO: task 25, humann____CSM5FZ4M : ready and waiting for resources 2017-07-18 18:28:24,131 LoggerReporter log_event INFO: task 25, humann____CSM5FZ4M : starting to run 2017-07-18 18:28:24,346 LoggerReporter task_command INFO: Tracked executable version: humann v3 2017-07-18 18:28:24,346 LoggerReporter task_command INFO: Executing with shell: humann --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5FZ4M.fastq --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main --o-log /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5FZ4M.log --threads 1 --taxonomic-profile /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main/CSM5FZ4M_taxonomic_profile.tsv 2017-07-18 18:32:42,958 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Output files will be written to: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main Found g__Haemophilus.s__Haemophilus_parainfluenzae : 15.89% of mapped reads Found g__Streptococcus.s__Streptococcus_vestibularis : 12.54% of mapped reads Found g__Streptococcus.s__Streptococcus_anginosus : 12.48% of mapped reads Found g__Escherichia.s__Escherichia_coli : 10.65% of mapped reads Found g__Faecalibacterium.s__Faecalibacterium_prausnitzii : 9.60% of mapped reads Found g__Bacteroides.s__Bacteroides_cellulosilyticus : 7.69% of mapped reads Found g__Bacteroides.s__Bacteroides_caccae : 7.22% of mapped reads Found g__Bacteroides.s__Bacteroides_thetaiotaomicron : 6.41% of mapped reads Found g__Bacteroides.s__Bacteroides_ovatus : 5.32% of mapped reads Found g__Bacteroides.s__Bacteroides_vulgatus : 4.04% of mapped reads Found g__Bacteroides.s__Bacteroides_xylanisolvens : 3.86% of mapped reads Found g__Parabacteroides.s__Parabacteroides_distasonis : 3.17% of mapped reads Found g__Blautia.s__Ruminococcus_torques : 1.11% of mapped reads Total species selected from prescreen: 13 Selected species explain 100.00% of predicted community composition Creating custom ChocoPhlAn database ........ Running bowtie2-build ........ Running bowtie2 ........ Total bugs from nucleotide alignment: 9 g__Bacteroides.s__Bacteroides_caccae: 16770 hits g__Parabacteroides.s__Parabacteroides_distasonis: 7725 hits g__Blautia.s__Ruminococcus_torques: 24 hits g__Bacteroides.s__Bacteroides_ovatus: 3786 hits g__Bacteroides.s__Bacteroides_cellulosilyticus: 2258 hits g__Bacteroides.s__Bacteroides_vulgatus: 714 hits g__Bacteroides.s__Bacteroides_thetaiotaomicron: 15798 hits g__Bacteroides.s__Bacteroides_xylanisolvens: 2058 hits g__Faecalibacterium.s__Faecalibacterium_prausnitzii: 5060 hits Total gene families from nucleotide alignment: 1532 Unaligned reads after nucleotide alignment: 49.7706018111 % Running diamond ........ Aligning to reference database: uniref90_demo_prots.dmnd Total bugs after translated alignment: 10 unclassified: 278187 hits g__Bacteroides.s__Bacteroides_caccae: 16770 hits g__Parabacteroides.s__Parabacteroides_distasonis: 7725 hits g__Blautia.s__Ruminococcus_torques: 24 hits g__Bacteroides.s__Bacteroides_ovatus: 3786 hits g__Bacteroides.s__Bacteroides_cellulosilyticus: 2258 hits g__Bacteroides.s__Bacteroides_vulgatus: 714 hits g__Bacteroides.s__Bacteroides_thetaiotaomicron: 15798 hits g__Bacteroides.s__Bacteroides_xylanisolvens: 2058 hits g__Faecalibacterium.s__Faecalibacterium_prausnitzii: 5060 hits Total gene families after translated alignment: 3569 Unaligned reads after translated alignment: 6.9190201222 % Computing gene families ... Computing pathways abundance and coverage ... Output files created: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5FZ4M_genefamilies.tsv /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5FZ4M_pathabundance.tsv /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5FZ4M_pathcoverage.tsv Stderr: 2017-07-18 18:32:42,959 LoggerReporter log_event INFO: task 25, humann____CSM5FZ4M : completed successfully 2017-07-18 18:32:42,960 LoggerReporter log_event INFO: task 32, humann_regroup_UniRef2EC____CSM5FZ4M : ready and waiting for resources 2017-07-18 18:32:42,960 LoggerReporter log_event INFO: task 32, humann_regroup_UniRef2EC____CSM5FZ4M : starting to run 2017-07-18 18:32:42,961 LoggerReporter task_command INFO: Executing with shell: humann_regroup_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5FZ4M_genefamilies.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5FZ4M_ecs.tsv --groups uniref90_level4ec 2017-07-18 18:32:43,733 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5FZ4M_genefamilies.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5FZ4M_genefamilies.tsv as stratified output, e.g. ['UniRef90_I9H3P2', 'g__Bacteroides.s__Bacteroides_caccae'] Loading mapping file from: /home/ljmciver/.local/lib/python2.7/site-packages/humann/data/misc/map_level4ec_uniref90.txt.gz Original Feature Count: 3570; Grouped 1+ times: 2078 (58.2%); Grouped 2+ times: 35 (1.0%) 2017-07-18 18:32:43,733 LoggerReporter log_event INFO: task 32, humann_regroup_UniRef2EC____CSM5FZ4M : completed successfully 2017-07-18 18:32:43,734 LoggerReporter log_event INFO: task 47, humann_renorm_ecs_relab____CSM5FZ4M : ready and waiting for resources 2017-07-18 18:32:43,734 LoggerReporter log_event INFO: task 47, humann_renorm_ecs_relab____CSM5FZ4M : starting to run 2017-07-18 18:32:43,735 LoggerReporter task_command INFO: Executing with shell: humann_renorm_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5FZ4M_ecs.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/ecs/CSM5FZ4M_ecs_relab.tsv --units relab --special n 2017-07-18 18:32:43,891 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5FZ4M_ecs.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5FZ4M_ecs.tsv as stratified output, e.g. ['UNGROUPED', 'g__Bacteroides.s__Bacteroides_caccae'] Excluding special feature: UNMAPPED Excluding special feature: UNGROUPED Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_caccae Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_cellulosilyticus Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_ovatus Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_thetaiotaomicron Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_vulgatus Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_xylanisolvens Excluding special feature: UNGROUPED|g__Blautia.s__Ruminococcus_torques Excluding special feature: UNGROUPED|g__Faecalibacterium.s__Faecalibacterium_prausnitzii Excluding special feature: UNGROUPED|g__Parabacteroides.s__Parabacteroides_distasonis Excluding special feature: UNGROUPED|unclassified 2017-07-18 18:32:43,892 LoggerReporter log_event INFO: task 47, humann_renorm_ecs_relab____CSM5FZ4M : completed successfully 2017-07-18 18:32:43,892 LoggerReporter log_event INFO: task 41, humann_renorm_genes_relab____CSM5FZ4M : ready and waiting for resources 2017-07-18 18:32:43,892 LoggerReporter log_event INFO: task 41, humann_renorm_genes_relab____CSM5FZ4M : starting to run 2017-07-18 18:32:43,892 LoggerReporter task_command INFO: Executing with shell: humann_renorm_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5FZ4M_genefamilies.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/genes/CSM5FZ4M_genefamilies_relab.tsv --units relab --special n 2017-07-18 18:32:44,127 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5FZ4M_genefamilies.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5FZ4M_genefamilies.tsv as stratified output, e.g. ['UniRef90_I9H3P2', 'g__Bacteroides.s__Bacteroides_caccae'] Excluding special feature: UNMAPPED 2017-07-18 18:32:44,128 LoggerReporter log_event INFO: task 41, humann_renorm_genes_relab____CSM5FZ4M : completed successfully 2017-07-18 18:32:44,128 LoggerReporter log_event INFO: task 53, humann_renorm_pathways_relab____CSM5FZ4M : ready and waiting for resources 2017-07-18 18:32:44,129 LoggerReporter log_event INFO: task 53, humann_renorm_pathways_relab____CSM5FZ4M : starting to run 2017-07-18 18:32:44,129 LoggerReporter task_command INFO: Executing with shell: humann_renorm_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5FZ4M_pathabundance.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/pathways/CSM5FZ4M_pathabundance_relab.tsv --units relab --special n 2017-07-18 18:32:44,317 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5FZ4M_pathabundance.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5FZ4M_pathabundance.tsv as stratified output, e.g. ['UNINTEGRATED', 'g__Bacteroides.s__Bacteroides_caccae'] Excluding special feature: UNMAPPED Excluding special feature: UNINTEGRATED Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_caccae Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_thetaiotaomicron Excluding special feature: UNINTEGRATED|unclassified Excluding special feature: UNINTEGRATED|g__Parabacteroides.s__Parabacteroides_distasonis Excluding special feature: UNINTEGRATED|g__Faecalibacterium.s__Faecalibacterium_prausnitzii Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_cellulosilyticus Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_ovatus Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_xylanisolvens Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_vulgatus 2017-07-18 18:32:44,318 LoggerReporter log_event INFO: task 53, humann_renorm_pathways_relab____CSM5FZ4M : completed successfully 2017-07-18 18:32:44,318 LoggerReporter log_event INFO: task 5, kneaddata____CSM5MCUO : ready and waiting for resources 2017-07-18 18:32:44,318 LoggerReporter log_event INFO: task 5, kneaddata____CSM5MCUO : starting to run 2017-07-18 18:32:44,465 LoggerReporter task_command INFO: Tracked executable version: kneaddata v0.6.1 2017-07-18 18:32:44,465 LoggerReporter task_command INFO: Executing with shell: kneaddata --input /work/code/biobakery_workflows/examples/tutorial/input/CSM5MCUO.fastq.gz --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main --threads 1 --output-prefix CSM5MCUO --reference-db /work/code/biobakery_workflows/examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/ --serial 2017-07-18 18:32:46,890 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Decompressing gzipped file ... Initial number of reads ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/decompressed_4AFJ8f_CSM5MCUO.fastq ): 27249 Running Trimmomatic ... Total reads after trimming ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCUO.trimmed.fastq ): 27183 Decontaminating ... Running bowtie2 ... Running bowtie2 ... Total reads after removing those found in reference database ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCUO_Homo_sapiens_demo_bowtie2_clean.fastq ): 27117 Total reads after merging results from multiple databases ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCUO.fastq ): 27063 Final output file created: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCUO.fastq Stderr: 2017-07-18 18:32:46,891 LoggerReporter log_event INFO: task 5, kneaddata____CSM5MCUO : completed successfully 2017-07-18 18:32:46,891 LoggerReporter log_event INFO: task 17, metaphlan____CSM5MCUO : ready and waiting for resources 2017-07-18 18:32:46,891 LoggerReporter log_event INFO: task 17, metaphlan____CSM5MCUO : starting to run 2017-07-18 18:32:46,979 LoggerReporter task_command INFO: Tracked executable version: MetaPhlAn version 3 2017-07-18 18:32:46,979 LoggerReporter task_command INFO: Executing with shell: metaphlan /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCUO.fastq --input_type fastq --output_file /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main/CSM5MCUO_taxonomic_profile.tsv --samout /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main/CSM5MCUO_bowtie2.sam --nproc 1 --no_map --tmp_dir /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main 2017-07-18 18:33:39,056 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: 2017-07-18 18:33:39,056 LoggerReporter log_event INFO: task 17, metaphlan____CSM5MCUO : completed successfully 2017-07-18 18:35:58,225 LoggerReporter log_event INFO: task 26, humann____CSM5MCUO : ready and waiting for resources 2017-07-18 18:35:58,225 LoggerReporter log_event INFO: task 26, humann____CSM5MCUO : starting to run 2017-07-18 18:35:58,381 LoggerReporter task_command INFO: Tracked executable version: humann v3 2017-07-18 18:35:58,382 LoggerReporter task_command INFO: Executing with shell: humann --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCUO.fastq --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main --o-log /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCUO.log --threads 1 --taxonomic-profile /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main/CSM5MCUO_taxonomic_profile.tsv 2017-07-18 18:40:14,597 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Output files will be written to: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main Found g__Faecalibacterium.s__Faecalibacterium_prausnitzii : 18.30% of mapped reads Found g__Escherichia.s__Escherichia_coli : 14.73% of mapped reads Found g__Klebsiella.s__Klebsiella_pneumoniae : 10.28% of mapped reads Found g__Bacteroides.s__Bacteroides_dorei : 9.95% of mapped reads Found g__Bacteroides.s__Bacteroides_thetaiotaomicron : 7.63% of mapped reads Found g__Bacteroides.s__Bacteroides_vulgatus : 7.57% of mapped reads Found g__Bacteroides.s__Bacteroides_ovatus : 7.36% of mapped reads Found g__Bacteroides.s__Bacteroides_xylanisolvens : 5.29% of mapped reads Found g__Bacteroides.s__Bacteroides_cellulosilyticus : 4.80% of mapped reads Found g__Parabacteroides.s__Parabacteroides_distasonis : 3.81% of mapped reads Found g__Blautia.s__Ruminococcus_obeum : 3.22% of mapped reads Found g__Dorea.s__Dorea_formicigenerans : 2.82% of mapped reads Found g__Bacteroides.s__Bacteroides_caccae : 1.88% of mapped reads Found g__Streptococcus.s__Streptococcus_salivarius : 1.07% of mapped reads Found g__Blautia.s__Ruminococcus_torques : 0.75% of mapped reads Found g__Haemophilus.s__Haemophilus_parainfluenzae : 0.56% of mapped reads Total species selected from prescreen: 16 Selected species explain 100.00% of predicted community composition Creating custom ChocoPhlAn database ........ Running bowtie2-build ........ Running bowtie2 ........ Total bugs from nucleotide alignment: 14 g__Streptococcus.s__Streptococcus_salivarius: 135 hits g__Klebsiella.s__Klebsiella_pneumoniae: 1080 hits g__Bacteroides.s__Bacteroides_dorei: 2312 hits g__Parabacteroides.s__Parabacteroides_distasonis: 704 hits g__Blautia.s__Ruminococcus_torques: 267 hits g__Bacteroides.s__Bacteroides_xylanisolvens: 1426 hits g__Bacteroides.s__Bacteroides_cellulosilyticus: 787 hits g__Bacteroides.s__Bacteroides_vulgatus: 2578 hits g__Bacteroides.s__Bacteroides_thetaiotaomicron: 1118 hits g__Blautia.s__Ruminococcus_obeum: 279 hits g__Bacteroides.s__Bacteroides_ovatus: 1458 hits g__Faecalibacterium.s__Faecalibacterium_prausnitzii: 10115 hits g__Dorea.s__Dorea_formicigenerans: 269 hits g__Bacteroides.s__Bacteroides_caccae: 260 hits Total gene families from nucleotide alignment: 2269 Unaligned reads after nucleotide alignment: 15.7964748919 % Running diamond ........ Aligning to reference database: uniref90_demo_prots.dmnd Total bugs after translated alignment: 15 g__Streptococcus.s__Streptococcus_salivarius: 135 hits unclassified: 15921 hits g__Klebsiella.s__Klebsiella_pneumoniae: 1080 hits g__Bacteroides.s__Bacteroides_dorei: 2312 hits g__Parabacteroides.s__Parabacteroides_distasonis: 704 hits g__Blautia.s__Ruminococcus_torques: 267 hits g__Bacteroides.s__Bacteroides_xylanisolvens: 1426 hits g__Bacteroides.s__Bacteroides_cellulosilyticus: 787 hits g__Bacteroides.s__Bacteroides_vulgatus: 2578 hits g__Bacteroides.s__Bacteroides_thetaiotaomicron: 1118 hits g__Blautia.s__Ruminococcus_obeum: 279 hits g__Bacteroides.s__Bacteroides_ovatus: 1458 hits g__Faecalibacterium.s__Faecalibacterium_prausnitzii: 10115 hits g__Dorea.s__Dorea_formicigenerans: 269 hits g__Bacteroides.s__Bacteroides_caccae: 260 hits Total gene families after translated alignment: 2912 Unaligned reads after translated alignment: 3.9869933119 % Computing gene families ... Computing pathways abundance and coverage ... Output files created: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCUO_genefamilies.tsv /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCUO_pathabundance.tsv /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCUO_pathcoverage.tsv Stderr: 2017-07-18 18:40:14,598 LoggerReporter log_event INFO: task 26, humann____CSM5MCUO : completed successfully 2017-07-18 18:40:14,599 LoggerReporter log_event INFO: task 33, humann_regroup_UniRef2EC____CSM5MCUO : ready and waiting for resources 2017-07-18 18:40:14,599 LoggerReporter log_event INFO: task 33, humann_regroup_UniRef2EC____CSM5MCUO : starting to run 2017-07-18 18:40:14,599 LoggerReporter task_command INFO: Executing with shell: humann_regroup_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCUO_genefamilies.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5MCUO_ecs.tsv --groups uniref90_level4ec 2017-07-18 18:40:15,379 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCUO_genefamilies.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCUO_genefamilies.tsv as stratified output, e.g. ['UniRef90_unknown', 'g__Faecalibacterium.s__Faecalibacterium_prausnitzii'] Loading mapping file from: /home/ljmciver/.local/lib/python2.7/site-packages/humann/data/misc/map_level4ec_uniref90.txt.gz Original Feature Count: 2913; Grouped 1+ times: 1020 (35.0%); Grouped 2+ times: 27 (0.9%) 2017-07-18 18:40:15,379 LoggerReporter log_event INFO: task 33, humann_regroup_UniRef2EC____CSM5MCUO : completed successfully 2017-07-18 18:40:15,379 LoggerReporter log_event INFO: task 48, humann_renorm_ecs_relab____CSM5MCUO : ready and waiting for resources 2017-07-18 18:40:15,379 LoggerReporter log_event INFO: task 48, humann_renorm_ecs_relab____CSM5MCUO : starting to run 2017-07-18 18:40:15,380 LoggerReporter task_command INFO: Executing with shell: humann_renorm_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5MCUO_ecs.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/ecs/CSM5MCUO_ecs_relab.tsv --units relab --special n 2017-07-18 18:40:15,561 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5MCUO_ecs.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5MCUO_ecs.tsv as stratified output, e.g. ['UNGROUPED', 'g__Bacteroides.s__Bacteroides_caccae'] Excluding special feature: UNMAPPED Excluding special feature: UNGROUPED Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_caccae Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_cellulosilyticus Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_dorei Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_ovatus Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_thetaiotaomicron Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_vulgatus Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_xylanisolvens Excluding special feature: UNGROUPED|g__Blautia.s__Ruminococcus_obeum Excluding special feature: UNGROUPED|g__Blautia.s__Ruminococcus_torques Excluding special feature: UNGROUPED|g__Dorea.s__Dorea_formicigenerans Excluding special feature: UNGROUPED|g__Faecalibacterium.s__Faecalibacterium_prausnitzii Excluding special feature: UNGROUPED|g__Klebsiella.s__Klebsiella_pneumoniae Excluding special feature: UNGROUPED|g__Parabacteroides.s__Parabacteroides_distasonis Excluding special feature: UNGROUPED|g__Streptococcus.s__Streptococcus_salivarius Excluding special feature: UNGROUPED|unclassified 2017-07-18 18:40:15,562 LoggerReporter log_event INFO: task 48, humann_renorm_ecs_relab____CSM5MCUO : completed successfully 2017-07-18 18:40:15,562 LoggerReporter log_event INFO: task 42, humann_renorm_genes_relab____CSM5MCUO : ready and waiting for resources 2017-07-18 18:40:15,562 LoggerReporter log_event INFO: task 42, humann_renorm_genes_relab____CSM5MCUO : starting to run 2017-07-18 18:40:15,562 LoggerReporter task_command INFO: Executing with shell: humann_renorm_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCUO_genefamilies.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/genes/CSM5MCUO_genefamilies_relab.tsv --units relab --special n 2017-07-18 18:40:15,758 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCUO_genefamilies.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCUO_genefamilies.tsv as stratified output, e.g. ['UniRef90_unknown', 'g__Faecalibacterium.s__Faecalibacterium_prausnitzii'] Excluding special feature: UNMAPPED 2017-07-18 18:40:15,758 LoggerReporter log_event INFO: task 42, humann_renorm_genes_relab____CSM5MCUO : completed successfully 2017-07-18 18:40:15,759 LoggerReporter log_event INFO: task 54, humann_renorm_pathways_relab____CSM5MCUO : ready and waiting for resources 2017-07-18 18:40:15,759 LoggerReporter log_event INFO: task 54, humann_renorm_pathways_relab____CSM5MCUO : starting to run 2017-07-18 18:40:15,760 LoggerReporter task_command INFO: Executing with shell: humann_renorm_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCUO_pathabundance.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/pathways/CSM5MCUO_pathabundance_relab.tsv --units relab --special n 2017-07-18 18:40:15,960 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCUO_pathabundance.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCUO_pathabundance.tsv as stratified output, e.g. ['UNINTEGRATED', 'g__Faecalibacterium.s__Faecalibacterium_prausnitzii'] Excluding special feature: UNMAPPED Excluding special feature: UNINTEGRATED Excluding special feature: UNINTEGRATED|g__Faecalibacterium.s__Faecalibacterium_prausnitzii Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_dorei Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_vulgatus Excluding special feature: UNINTEGRATED|g__Klebsiella.s__Klebsiella_pneumoniae Excluding special feature: UNINTEGRATED|unclassified Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_xylanisolvens Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_thetaiotaomicron Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_cellulosilyticus Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_ovatus Excluding special feature: UNINTEGRATED|g__Parabacteroides.s__Parabacteroides_distasonis Excluding special feature: UNINTEGRATED|g__Dorea.s__Dorea_formicigenerans Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_caccae Excluding special feature: UNINTEGRATED|g__Blautia.s__Ruminococcus_torques 2017-07-18 18:40:15,961 LoggerReporter log_event INFO: task 54, humann_renorm_pathways_relab____CSM5MCUO : completed successfully 2017-07-18 18:40:15,962 LoggerReporter log_event INFO: task 7, kneaddata____CSM5MCVL : ready and waiting for resources 2017-07-18 18:40:15,962 LoggerReporter log_event INFO: task 7, kneaddata____CSM5MCVL : starting to run 2017-07-18 18:40:16,110 LoggerReporter task_command INFO: Tracked executable version: kneaddata v0.6.1 2017-07-18 18:40:16,110 LoggerReporter task_command INFO: Executing with shell: kneaddata --input /work/code/biobakery_workflows/examples/tutorial/input/CSM5MCVL.fastq.gz --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main --threads 1 --output-prefix CSM5MCVL --reference-db /work/code/biobakery_workflows/examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/ --serial 2017-07-18 18:40:18,423 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Decompressing gzipped file ... Initial number of reads ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/decompressed_v3Jlf2_CSM5MCVL.fastq ): 30251 Running Trimmomatic ... Total reads after trimming ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCVL.trimmed.fastq ): 30144 Decontaminating ... Running bowtie2 ... Running bowtie2 ... Total reads after removing those found in reference database ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCVL_Homo_sapiens_demo_bowtie2_clean.fastq ): 30076 Total reads after merging results from multiple databases ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCVL.fastq ): 29991 Final output file created: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCVL.fastq Stderr: 2017-07-18 18:40:18,423 LoggerReporter log_event INFO: task 7, kneaddata____CSM5MCVL : completed successfully 2017-07-18 18:40:18,423 LoggerReporter log_event INFO: task 18, metaphlan____CSM5MCVL : ready and waiting for resources 2017-07-18 18:40:18,424 LoggerReporter log_event INFO: task 18, metaphlan____CSM5MCVL : starting to run 2017-07-18 18:40:18,509 LoggerReporter task_command INFO: Tracked executable version: MetaPhlAn version 3 2017-07-18 18:40:18,509 LoggerReporter task_command INFO: Executing with shell: metaphlan /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCVL.fastq --input_type fastq --output_file /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main/CSM5MCVL_taxonomic_profile.tsv --samout /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main/CSM5MCVL_bowtie2.sam --nproc 1 --no_map --tmp_dir /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main 2017-07-18 18:41:11,011 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: 2017-07-18 18:41:11,012 LoggerReporter log_event INFO: task 18, metaphlan____CSM5MCVL : completed successfully 2017-07-18 18:43:50,517 LoggerReporter log_event INFO: task 27, humann____CSM5MCVL : ready and waiting for resources 2017-07-18 18:43:50,517 LoggerReporter log_event INFO: task 27, humann____CSM5MCVL : starting to run 2017-07-18 18:43:50,667 LoggerReporter task_command INFO: Tracked executable version: humann v3 2017-07-18 18:43:50,667 LoggerReporter task_command INFO: Executing with shell: humann --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCVL.fastq --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main --o-log /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVL.log --threads 1 --taxonomic-profile /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main/CSM5MCVL_taxonomic_profile.tsv 2017-07-18 18:49:03,033 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Output files will be written to: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main Found g__Faecalibacterium.s__Faecalibacterium_prausnitzii : 11.98% of mapped reads Found g__Escherichia.s__Escherichia_coli : 9.09% of mapped reads Found g__Blautia.s__Ruminococcus_gnavus : 6.21% of mapped reads Found g__Bacteroides.s__Bacteroides_caccae : 6.09% of mapped reads Found g__Bacteroides.s__Bacteroides_dorei : 5.98% of mapped reads Found g__Bacteroides.s__Bacteroides_vulgatus : 5.91% of mapped reads Found g__Bacteroides.s__Bacteroides_finegoldii : 5.72% of mapped reads Found g__Bifidobacterium.s__Bifidobacterium_longum : 5.36% of mapped reads Found g__Bacteroides.s__Bacteroides_ovatus : 5.11% of mapped reads Found g__Bacteroides.s__Bacteroides_fragilis : 4.97% of mapped reads Found g__Klebsiella.s__Klebsiella_pneumoniae : 4.84% of mapped reads Found g__Parabacteroides.s__Parabacteroides_distasonis : 4.28% of mapped reads Found g__Blautia.s__Ruminococcus_obeum : 3.88% of mapped reads Found g__Bacteroides.s__Bacteroides_cellulosilyticus : 3.81% of mapped reads Found g__Bacteroides.s__Bacteroides_thetaiotaomicron : 3.43% of mapped reads Found g__Blautia.s__Ruminococcus_torques : 2.95% of mapped reads Found g__Dorea.s__Dorea_formicigenerans : 2.94% of mapped reads Found g__Haemophilus.s__Haemophilus_parainfluenzae : 2.66% of mapped reads Found g__Streptococcus.s__Streptococcus_salivarius : 2.53% of mapped reads Found g__Bacteroides.s__Bacteroides_xylanisolvens : 2.27% of mapped reads Total species selected from prescreen: 20 Selected species explain 100.00% of predicted community composition Creating custom ChocoPhlAn database ........ Running bowtie2-build ........ Running bowtie2 ........ Total bugs from nucleotide alignment: 18 g__Streptococcus.s__Streptococcus_salivarius: 463 hits g__Klebsiella.s__Klebsiella_pneumoniae: 611 hits g__Bacteroides.s__Bacteroides_caccae: 1713 hits g__Parabacteroides.s__Parabacteroides_distasonis: 851 hits g__Bacteroides.s__Bacteroides_thetaiotaomicron: 678 hits g__Blautia.s__Ruminococcus_torques: 342 hits g__Bacteroides.s__Bacteroides_ovatus: 1525 hits g__Bacteroides.s__Bacteroides_finegoldii: 1502 hits g__Bacteroides.s__Bacteroides_cellulosilyticus: 689 hits g__Bacteroides.s__Bacteroides_vulgatus: 7012 hits g__Dorea.s__Dorea_formicigenerans: 420 hits g__Bacteroides.s__Bacteroides_xylanisolvens: 606 hits g__Blautia.s__Ruminococcus_obeum: 554 hits g__Bacteroides.s__Bacteroides_fragilis: 970 hits g__Faecalibacterium.s__Faecalibacterium_prausnitzii: 6821 hits g__Bifidobacterium.s__Bifidobacterium_longum: 773 hits g__Blautia.s__Ruminococcus_gnavus: 854 hits g__Bacteroides.s__Bacteroides_dorei: 1796 hits Total gene families from nucleotide alignment: 3365 Unaligned reads after nucleotide alignment: 6.0384782101 % Running diamond ........ Aligning to reference database: uniref90_demo_prots.dmnd Total bugs after translated alignment: 19 g__Streptococcus.s__Streptococcus_salivarius: 463 hits unclassified: 1039 hits g__Klebsiella.s__Klebsiella_pneumoniae: 611 hits g__Bacteroides.s__Bacteroides_caccae: 1713 hits g__Parabacteroides.s__Parabacteroides_distasonis: 851 hits g__Bacteroides.s__Bacteroides_thetaiotaomicron: 678 hits g__Blautia.s__Ruminococcus_torques: 342 hits g__Bacteroides.s__Bacteroides_ovatus: 1525 hits g__Bacteroides.s__Bacteroides_finegoldii: 1502 hits g__Bacteroides.s__Bacteroides_cellulosilyticus: 689 hits g__Bacteroides.s__Bacteroides_vulgatus: 7012 hits g__Dorea.s__Dorea_formicigenerans: 420 hits g__Bacteroides.s__Bacteroides_xylanisolvens: 606 hits g__Blautia.s__Ruminococcus_obeum: 554 hits g__Bacteroides.s__Bacteroides_fragilis: 970 hits g__Faecalibacterium.s__Faecalibacterium_prausnitzii: 6821 hits g__Bifidobacterium.s__Bifidobacterium_longum: 773 hits g__Blautia.s__Ruminococcus_gnavus: 854 hits g__Bacteroides.s__Bacteroides_dorei: 1796 hits Total gene families after translated alignment: 3487 Unaligned reads after translated alignment: 4.5680370778 % Computing gene families ... Computing pathways abundance and coverage ... Output files created: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVL_genefamilies.tsv /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVL_pathabundance.tsv /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVL_pathcoverage.tsv Stderr: 2017-07-18 18:49:03,033 LoggerReporter log_event INFO: task 27, humann____CSM5MCVL : completed successfully 2017-07-18 18:49:03,033 LoggerReporter log_event INFO: task 34, humann_regroup_UniRef2EC____CSM5MCVL : ready and waiting for resources 2017-07-18 18:49:03,034 LoggerReporter log_event INFO: task 34, humann_regroup_UniRef2EC____CSM5MCVL : starting to run 2017-07-18 18:49:03,034 LoggerReporter task_command INFO: Executing with shell: humann_regroup_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVL_genefamilies.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5MCVL_ecs.tsv --groups uniref90_level4ec 2017-07-18 18:49:03,711 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVL_genefamilies.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVL_genefamilies.tsv as stratified output, e.g. ['UniRef90_R9H3J9', 'g__Bacteroides.s__Bacteroides_vulgatus'] Loading mapping file from: /home/ljmciver/.local/lib/python2.7/site-packages/humann/data/misc/map_level4ec_uniref90.txt.gz Original Feature Count: 3488; Grouped 1+ times: 807 (23.1%); Grouped 2+ times: 8 (0.2%) 2017-07-18 18:49:03,711 LoggerReporter log_event INFO: task 34, humann_regroup_UniRef2EC____CSM5MCVL : completed successfully 2017-07-18 18:49:03,711 LoggerReporter log_event INFO: task 49, humann_renorm_ecs_relab____CSM5MCVL : ready and waiting for resources 2017-07-18 18:49:03,711 LoggerReporter log_event INFO: task 49, humann_renorm_ecs_relab____CSM5MCVL : starting to run 2017-07-18 18:49:03,711 LoggerReporter task_command INFO: Executing with shell: humann_renorm_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5MCVL_ecs.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/ecs/CSM5MCVL_ecs_relab.tsv --units relab --special n 2017-07-18 18:49:03,859 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5MCVL_ecs.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5MCVL_ecs.tsv as stratified output, e.g. ['UNGROUPED', 'g__Bacteroides.s__Bacteroides_caccae'] Excluding special feature: UNMAPPED Excluding special feature: UNGROUPED Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_caccae Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_cellulosilyticus Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_dorei Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_finegoldii Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_fragilis Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_ovatus Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_thetaiotaomicron Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_vulgatus Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_xylanisolvens Excluding special feature: UNGROUPED|g__Bifidobacterium.s__Bifidobacterium_longum Excluding special feature: UNGROUPED|g__Blautia.s__Ruminococcus_gnavus Excluding special feature: UNGROUPED|g__Blautia.s__Ruminococcus_obeum Excluding special feature: UNGROUPED|g__Blautia.s__Ruminococcus_torques Excluding special feature: UNGROUPED|g__Dorea.s__Dorea_formicigenerans Excluding special feature: UNGROUPED|g__Faecalibacterium.s__Faecalibacterium_prausnitzii Excluding special feature: UNGROUPED|g__Klebsiella.s__Klebsiella_pneumoniae Excluding special feature: UNGROUPED|g__Parabacteroides.s__Parabacteroides_distasonis Excluding special feature: UNGROUPED|g__Streptococcus.s__Streptococcus_salivarius Excluding special feature: UNGROUPED|unclassified 2017-07-18 18:49:03,860 LoggerReporter log_event INFO: task 49, humann_renorm_ecs_relab____CSM5MCVL : completed successfully 2017-07-18 18:49:03,860 LoggerReporter log_event INFO: task 43, humann_renorm_genes_relab____CSM5MCVL : ready and waiting for resources 2017-07-18 18:49:03,860 LoggerReporter log_event INFO: task 43, humann_renorm_genes_relab____CSM5MCVL : starting to run 2017-07-18 18:49:03,860 LoggerReporter task_command INFO: Executing with shell: humann_renorm_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVL_genefamilies.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/genes/CSM5MCVL_genefamilies_relab.tsv --units relab --special n 2017-07-18 18:49:04,063 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVL_genefamilies.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVL_genefamilies.tsv as stratified output, e.g. ['UniRef90_R9H3J9', 'g__Bacteroides.s__Bacteroides_vulgatus'] Excluding special feature: UNMAPPED 2017-07-18 18:49:04,064 LoggerReporter log_event INFO: task 43, humann_renorm_genes_relab____CSM5MCVL : completed successfully 2017-07-18 18:49:04,064 LoggerReporter log_event INFO: task 55, humann_renorm_pathways_relab____CSM5MCVL : ready and waiting for resources 2017-07-18 18:49:04,064 LoggerReporter log_event INFO: task 55, humann_renorm_pathways_relab____CSM5MCVL : starting to run 2017-07-18 18:49:04,064 LoggerReporter task_command INFO: Executing with shell: humann_renorm_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVL_pathabundance.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/pathways/CSM5MCVL_pathabundance_relab.tsv --units relab --special n 2017-07-18 18:49:04,211 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVL_pathabundance.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVL_pathabundance.tsv as stratified output, e.g. ['UNINTEGRATED', 'g__Bacteroides.s__Bacteroides_vulgatus'] Excluding special feature: UNMAPPED Excluding special feature: UNINTEGRATED Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_vulgatus Excluding special feature: UNINTEGRATED|g__Faecalibacterium.s__Faecalibacterium_prausnitzii Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_dorei Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_caccae Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_finegoldii Excluding special feature: UNINTEGRATED|g__Klebsiella.s__Klebsiella_pneumoniae Excluding special feature: UNINTEGRATED|g__Dorea.s__Dorea_formicigenerans Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_ovatus Excluding special feature: UNINTEGRATED|g__Parabacteroides.s__Parabacteroides_distasonis Excluding special feature: UNINTEGRATED|g__Blautia.s__Ruminococcus_gnavus Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_cellulosilyticus Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_fragilis Excluding special feature: UNINTEGRATED|unclassified Excluding special feature: UNINTEGRATED|g__Bifidobacterium.s__Bifidobacterium_longum Excluding special feature: UNINTEGRATED|g__Blautia.s__Ruminococcus_obeum Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_xylanisolvens Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_thetaiotaomicron Excluding special feature: UNINTEGRATED|g__Streptococcus.s__Streptococcus_salivarius Excluding special feature: UNINTEGRATED|g__Blautia.s__Ruminococcus_torques 2017-07-18 18:49:04,212 LoggerReporter log_event INFO: task 55, humann_renorm_pathways_relab____CSM5MCVL : completed successfully 2017-07-18 18:49:04,212 LoggerReporter log_event INFO: task 9, kneaddata____CSM5MCVN : ready and waiting for resources 2017-07-18 18:49:04,213 LoggerReporter log_event INFO: task 9, kneaddata____CSM5MCVN : starting to run 2017-07-18 18:49:04,352 LoggerReporter task_command INFO: Tracked executable version: kneaddata v0.6.1 2017-07-18 18:49:04,353 LoggerReporter task_command INFO: Executing with shell: kneaddata --input /work/code/biobakery_workflows/examples/tutorial/input/CSM5MCVN.fastq.gz --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main --threads 1 --output-prefix CSM5MCVN --reference-db /work/code/biobakery_workflows/examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/ --serial 2017-07-18 18:49:10,515 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Decompressing gzipped file ... Initial number of reads ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/decompressed_FCjRod_CSM5MCVN.fastq ): 86293 Running Trimmomatic ... Total reads after trimming ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCVN.trimmed.fastq ): 86209 Decontaminating ... Running bowtie2 ... Running bowtie2 ... Total reads after removing those found in reference database ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCVN_Homo_sapiens_demo_bowtie2_clean.fastq ): 86122 Total reads after merging results from multiple databases ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCVN.fastq ): 86039 Final output file created: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCVN.fastq Stderr: 2017-07-18 18:49:10,516 LoggerReporter log_event INFO: task 9, kneaddata____CSM5MCVN : completed successfully 2017-07-18 18:49:10,516 LoggerReporter log_event INFO: task 19, metaphlan____CSM5MCVN : ready and waiting for resources 2017-07-18 18:49:10,516 LoggerReporter log_event INFO: task 19, metaphlan____CSM5MCVN : starting to run 2017-07-18 18:49:10,592 LoggerReporter task_command INFO: Tracked executable version: MetaPhlAn version 3 2017-07-18 18:49:10,592 LoggerReporter task_command INFO: Executing with shell: metaphlan /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCVN.fastq --input_type fastq --output_file /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main/CSM5MCVN_taxonomic_profile.tsv --samout /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main/CSM5MCVN_bowtie2.sam --nproc 1 --no_map --tmp_dir /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main 2017-07-18 18:50:06,354 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: 2017-07-18 18:50:06,354 LoggerReporter log_event INFO: task 19, metaphlan____CSM5MCVN : completed successfully 2017-07-18 18:52:33,113 LoggerReporter log_event INFO: task 28, humann____CSM5MCVN : ready and waiting for resources 2017-07-18 18:52:33,113 LoggerReporter log_event INFO: task 28, humann____CSM5MCVN : starting to run 2017-07-18 18:52:33,270 LoggerReporter task_command INFO: Tracked executable version: humann v3 2017-07-18 18:52:33,271 LoggerReporter task_command INFO: Executing with shell: humann --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCVN.fastq --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main --o-log /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVN.log --threads 1 --taxonomic-profile /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main/CSM5MCVN_taxonomic_profile.tsv 2017-07-18 18:56:43,560 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Output files will be written to: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main Found g__Lactobacillus.s__Lactobacillus_salivarius : 13.30% of mapped reads Found g__Haemophilus.s__Haemophilus_parainfluenzae : 13.25% of mapped reads Found g__Faecalibacterium.s__Faecalibacterium_prausnitzii : 12.01% of mapped reads Found g__Streptococcus.s__Streptococcus_vestibularis : 10.47% of mapped reads Found g__Bacteroides.s__Bacteroides_thetaiotaomicron : 7.41% of mapped reads Found g__Bacteroides.s__Bacteroides_ovatus : 6.43% of mapped reads Found g__Bacteroides.s__Bacteroides_caccae : 6.34% of mapped reads Found g__Blautia.s__Ruminococcus_torques : 6.25% of mapped reads Found g__Bacteroides.s__Bacteroides_vulgatus : 5.60% of mapped reads Found g__Bifidobacterium.s__Bifidobacterium_longum : 3.94% of mapped reads Found g__Streptococcus.s__Streptococcus_anginosus : 3.57% of mapped reads Found g__Bifidobacterium.s__Bifidobacterium_dentium : 3.36% of mapped reads Found g__Parabacteroides.s__Parabacteroides_distasonis : 2.86% of mapped reads Found g__Bacteroides.s__Bacteroides_xylanisolvens : 1.85% of mapped reads Found g__Escherichia.s__Escherichia_coli : 1.74% of mapped reads Found g__Bacteroides.s__Bacteroides_dorei : 1.62% of mapped reads Total species selected from prescreen: 16 Selected species explain 100.00% of predicted community composition Creating custom ChocoPhlAn database ........ Running bowtie2-build ........ Running bowtie2 ........ Total bugs from nucleotide alignment: 11 g__Bifidobacterium.s__Bifidobacterium_dentium: 457 hits g__Bacteroides.s__Bacteroides_dorei: 2111 hits g__Parabacteroides.s__Parabacteroides_distasonis: 2128 hits g__Blautia.s__Ruminococcus_torques: 809 hits g__Bacteroides.s__Bacteroides_ovatus: 6192 hits g__Bacteroides.s__Bacteroides_vulgatus: 17554 hits g__Bacteroides.s__Bacteroides_thetaiotaomicron: 2891 hits g__Bacteroides.s__Bacteroides_xylanisolvens: 1113 hits g__Faecalibacterium.s__Faecalibacterium_prausnitzii: 5642 hits g__Bifidobacterium.s__Bifidobacterium_longum: 521 hits g__Bacteroides.s__Bacteroides_caccae: 1711 hits Total gene families from nucleotide alignment: 1854 Unaligned reads after nucleotide alignment: 52.1972593824 % Running diamond ........ Aligning to reference database: uniref90_demo_prots.dmnd Total bugs after translated alignment: 12 g__Bifidobacterium.s__Bifidobacterium_dentium: 457 hits g__Bacteroides.s__Bacteroides_dorei: 2111 hits g__Parabacteroides.s__Parabacteroides_distasonis: 2128 hits g__Blautia.s__Ruminococcus_torques: 809 hits g__Bacteroides.s__Bacteroides_ovatus: 6192 hits unclassified: 143915 hits g__Bacteroides.s__Bacteroides_vulgatus: 17554 hits g__Bacteroides.s__Bacteroides_thetaiotaomicron: 2891 hits g__Bacteroides.s__Bacteroides_xylanisolvens: 1113 hits g__Faecalibacterium.s__Faecalibacterium_prausnitzii: 5642 hits g__Bifidobacterium.s__Bifidobacterium_longum: 521 hits g__Bacteroides.s__Bacteroides_caccae: 1711 hits Total gene families after translated alignment: 2895 Unaligned reads after translated alignment: 8.5600715954 % Computing gene families ... Computing pathways abundance and coverage ... Output files created: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVN_genefamilies.tsv /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVN_pathabundance.tsv /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVN_pathcoverage.tsv Stderr: 2017-07-18 18:56:43,561 LoggerReporter log_event INFO: task 28, humann____CSM5MCVN : completed successfully 2017-07-18 18:56:43,561 LoggerReporter log_event INFO: task 35, humann_regroup_UniRef2EC____CSM5MCVN : ready and waiting for resources 2017-07-18 18:56:43,561 LoggerReporter log_event INFO: task 35, humann_regroup_UniRef2EC____CSM5MCVN : starting to run 2017-07-18 18:56:43,561 LoggerReporter task_command INFO: Executing with shell: humann_regroup_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVN_genefamilies.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5MCVN_ecs.tsv --groups uniref90_level4ec 2017-07-18 18:56:44,239 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVN_genefamilies.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVN_genefamilies.tsv as stratified output, e.g. ['UniRef90_R9H3J9', 'g__Bacteroides.s__Bacteroides_vulgatus'] Loading mapping file from: /home/ljmciver/.local/lib/python2.7/site-packages/humann/data/misc/map_level4ec_uniref90.txt.gz Original Feature Count: 2896; Grouped 1+ times: 1315 (45.4%); Grouped 2+ times: 6 (0.2%) 2017-07-18 18:56:44,239 LoggerReporter log_event INFO: task 35, humann_regroup_UniRef2EC____CSM5MCVN : completed successfully 2017-07-18 18:56:44,240 LoggerReporter log_event INFO: task 50, humann_renorm_ecs_relab____CSM5MCVN : ready and waiting for resources 2017-07-18 18:56:44,240 LoggerReporter log_event INFO: task 50, humann_renorm_ecs_relab____CSM5MCVN : starting to run 2017-07-18 18:56:44,240 LoggerReporter task_command INFO: Executing with shell: humann_renorm_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5MCVN_ecs.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/ecs/CSM5MCVN_ecs_relab.tsv --units relab --special n 2017-07-18 18:56:44,452 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5MCVN_ecs.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5MCVN_ecs.tsv as stratified output, e.g. ['UNGROUPED', 'g__Bacteroides.s__Bacteroides_caccae'] Excluding special feature: UNMAPPED Excluding special feature: UNGROUPED Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_caccae Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_dorei Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_ovatus Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_thetaiotaomicron Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_vulgatus Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_xylanisolvens Excluding special feature: UNGROUPED|g__Bifidobacterium.s__Bifidobacterium_dentium Excluding special feature: UNGROUPED|g__Bifidobacterium.s__Bifidobacterium_longum Excluding special feature: UNGROUPED|g__Blautia.s__Ruminococcus_torques Excluding special feature: UNGROUPED|g__Faecalibacterium.s__Faecalibacterium_prausnitzii Excluding special feature: UNGROUPED|g__Parabacteroides.s__Parabacteroides_distasonis Excluding special feature: UNGROUPED|unclassified 2017-07-18 18:56:44,453 LoggerReporter log_event INFO: task 50, humann_renorm_ecs_relab____CSM5MCVN : completed successfully 2017-07-18 18:56:44,454 LoggerReporter log_event INFO: task 44, humann_renorm_genes_relab____CSM5MCVN : ready and waiting for resources 2017-07-18 18:56:44,454 LoggerReporter log_event INFO: task 44, humann_renorm_genes_relab____CSM5MCVN : starting to run 2017-07-18 18:56:44,455 LoggerReporter task_command INFO: Executing with shell: humann_renorm_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVN_genefamilies.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/genes/CSM5MCVN_genefamilies_relab.tsv --units relab --special n 2017-07-18 18:56:44,691 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVN_genefamilies.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVN_genefamilies.tsv as stratified output, e.g. ['UniRef90_R9H3J9', 'g__Bacteroides.s__Bacteroides_vulgatus'] Excluding special feature: UNMAPPED 2017-07-18 18:56:44,691 LoggerReporter log_event INFO: task 44, humann_renorm_genes_relab____CSM5MCVN : completed successfully 2017-07-18 18:56:44,692 LoggerReporter log_event INFO: task 56, humann_renorm_pathways_relab____CSM5MCVN : ready and waiting for resources 2017-07-18 18:56:44,692 LoggerReporter log_event INFO: task 56, humann_renorm_pathways_relab____CSM5MCVN : starting to run 2017-07-18 18:56:44,692 LoggerReporter task_command INFO: Executing with shell: humann_renorm_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVN_pathabundance.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/pathways/CSM5MCVN_pathabundance_relab.tsv --units relab --special n 2017-07-18 18:56:44,904 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVN_pathabundance.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCVN_pathabundance.tsv as stratified output, e.g. ['UNINTEGRATED', 'g__Bacteroides.s__Bacteroides_vulgatus'] Excluding special feature: UNMAPPED Excluding special feature: UNINTEGRATED Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_vulgatus Excluding special feature: UNINTEGRATED|unclassified Excluding special feature: UNINTEGRATED|g__Faecalibacterium.s__Faecalibacterium_prausnitzii Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_ovatus Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_thetaiotaomicron Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_caccae Excluding special feature: UNINTEGRATED|g__Parabacteroides.s__Parabacteroides_distasonis Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_dorei Excluding special feature: UNINTEGRATED|g__Bifidobacterium.s__Bifidobacterium_longum Excluding special feature: UNINTEGRATED|g__Blautia.s__Ruminococcus_torques Excluding special feature: UNINTEGRATED|g__Bifidobacterium.s__Bifidobacterium_dentium Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_xylanisolvens 2017-07-18 18:56:44,905 LoggerReporter log_event INFO: task 56, humann_renorm_pathways_relab____CSM5MCVN : completed successfully 2017-07-18 18:56:44,905 LoggerReporter log_event INFO: task 11, kneaddata____CSM5MCW6 : ready and waiting for resources 2017-07-18 18:56:44,905 LoggerReporter log_event INFO: task 11, kneaddata____CSM5MCW6 : starting to run 2017-07-18 18:56:45,052 LoggerReporter task_command INFO: Tracked executable version: kneaddata v0.6.1 2017-07-18 18:56:45,052 LoggerReporter task_command INFO: Executing with shell: kneaddata --input /work/code/biobakery_workflows/examples/tutorial/input/CSM5MCW6.fastq.gz --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main --threads 1 --output-prefix CSM5MCW6 --reference-db /work/code/biobakery_workflows/examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/ --serial 2017-07-18 18:56:47,344 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Decompressing gzipped file ... Initial number of reads ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/decompressed_bO7Y16_CSM5MCW6.fastq ): 35200 Running Trimmomatic ... Total reads after trimming ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCW6.trimmed.fastq ): 35104 Decontaminating ... Running bowtie2 ... Running bowtie2 ... Total reads after removing those found in reference database ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCW6_Homo_sapiens_demo_bowtie2_clean.fastq ): 35031 Total reads after merging results from multiple databases ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCW6.fastq ): 34935 Final output file created: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCW6.fastq Stderr: 2017-07-18 18:56:47,344 LoggerReporter log_event INFO: task 11, kneaddata____CSM5MCW6 : completed successfully 2017-07-18 18:56:47,344 LoggerReporter log_event INFO: task 20, metaphlan____CSM5MCW6 : ready and waiting for resources 2017-07-18 18:56:47,345 LoggerReporter log_event INFO: task 20, metaphlan____CSM5MCW6 : starting to run 2017-07-18 18:56:47,493 LoggerReporter task_command INFO: Tracked executable version: MetaPhlAn version 3 2017-07-18 18:56:47,494 LoggerReporter task_command INFO: Executing with shell: metaphlan.py /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCW6.fastq --input_type fastq --output_file /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main/CSM5MCW6_taxonomic_profile.tsv --samout /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main/CSM5MCW6_bowtie2.sam --nproc 1 --no_map --tmp_dir /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main 2017-07-18 18:57:41,346 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: 2017-07-18 18:57:41,346 LoggerReporter log_event INFO: task 20, metaphlan____CSM5MCW6 : completed successfully 2017-07-18 19:00:23,684 LoggerReporter log_event INFO: task 29, humann____CSM5MCW6 : ready and waiting for resources 2017-07-18 19:00:23,684 LoggerReporter log_event INFO: task 29, humann____CSM5MCW6 : starting to run 2017-07-18 19:00:23,890 LoggerReporter task_command INFO: Tracked executable version: humann v3 2017-07-18 19:00:23,890 LoggerReporter task_command INFO: Executing with shell: humann --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCW6.fastq --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main --o-log /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCW6.log --threads 1 --taxonomic-profile /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main/CSM5MCW6_taxonomic_profile.tsv 2017-07-18 19:04:34,401 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Output files will be written to: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main Found g__Faecalibacterium.s__Faecalibacterium_prausnitzii : 12.09% of mapped reads Found g__Bacteroides.s__Bacteroides_fragilis : 7.80% of mapped reads Found g__Bacteroides.s__Bacteroides_cellulosilyticus : 7.22% of mapped reads Found g__Bacteroides.s__Bacteroides_caccae : 6.91% of mapped reads Found g__Bacteroides.s__Bacteroides_dorei : 6.74% of mapped reads Found g__Bifidobacterium.s__Bifidobacterium_longum : 6.43% of mapped reads Found g__Bacteroides.s__Bacteroides_vulgatus : 6.42% of mapped reads Found g__Parabacteroides.s__Parabacteroides_distasonis : 6.41% of mapped reads Found g__Blautia.s__Ruminococcus_obeum : 6.23% of mapped reads Found g__Bacteroides.s__Bacteroides_thetaiotaomicron : 6.22% of mapped reads Found g__Streptococcus.s__Streptococcus_salivarius : 5.98% of mapped reads Found g__Bacteroides.s__Bacteroides_ovatus : 5.97% of mapped reads Found g__Blautia.s__Ruminococcus_torques : 4.98% of mapped reads Found g__Dorea.s__Dorea_formicigenerans : 4.86% of mapped reads Found g__Bacteroides.s__Bacteroides_finegoldii : 3.40% of mapped reads Found g__Streptococcus.s__Streptococcus_parasanguinis : 1.85% of mapped reads Found g__Streptococcus.s__Streptococcus_vestibularis : 0.47% of mapped reads Total species selected from prescreen: 17 Selected species explain 100.00% of predicted community composition Creating custom ChocoPhlAn database ........ Running bowtie2-build ........ Running bowtie2 ........ Total bugs from nucleotide alignment: 16 g__Streptococcus.s__Streptococcus_salivarius: 1196 hits g__Bacteroides.s__Bacteroides_caccae: 3455 hits g__Parabacteroides.s__Parabacteroides_distasonis: 1950 hits g__Bacteroides.s__Bacteroides_thetaiotaomicron: 2072 hits g__Blautia.s__Ruminococcus_torques: 559 hits g__Bacteroides.s__Bacteroides_ovatus: 2635 hits g__Bacteroides.s__Bacteroides_finegoldii: 696 hits g__Bacteroides.s__Bacteroides_cellulosilyticus: 1392 hits g__Bacteroides.s__Bacteroides_vulgatus: 1722 hits g__Bacteroides.s__Bacteroides_fragilis: 3306 hits g__Blautia.s__Ruminococcus_obeum: 770 hits g__Faecalibacterium.s__Faecalibacterium_prausnitzii: 10503 hits g__Streptococcus.s__Streptococcus_parasanguinis: 231 hits g__Dorea.s__Dorea_formicigenerans: 645 hits g__Bifidobacterium.s__Bifidobacterium_longum: 899 hits g__Bacteroides.s__Bacteroides_dorei: 1497 hits Total gene families from nucleotide alignment: 3223 Unaligned reads after nucleotide alignment: 4.0274796050 % Running diamond ........ Aligning to reference database: uniref90_demo_prots.dmnd Total bugs after translated alignment: 17 g__Streptococcus.s__Streptococcus_salivarius: 1196 hits unclassified: 328 hits g__Bacteroides.s__Bacteroides_caccae: 3455 hits g__Parabacteroides.s__Parabacteroides_distasonis: 1950 hits g__Bacteroides.s__Bacteroides_thetaiotaomicron: 2072 hits g__Blautia.s__Ruminococcus_torques: 559 hits g__Bacteroides.s__Bacteroides_ovatus: 2635 hits g__Bacteroides.s__Bacteroides_finegoldii: 696 hits g__Bacteroides.s__Bacteroides_cellulosilyticus: 1392 hits g__Bacteroides.s__Bacteroides_vulgatus: 1722 hits g__Bacteroides.s__Bacteroides_fragilis: 3306 hits g__Blautia.s__Ruminococcus_obeum: 770 hits g__Faecalibacterium.s__Faecalibacterium_prausnitzii: 10503 hits g__Streptococcus.s__Streptococcus_parasanguinis: 231 hits g__Dorea.s__Dorea_formicigenerans: 645 hits g__Bifidobacterium.s__Bifidobacterium_longum: 899 hits g__Bacteroides.s__Bacteroides_dorei: 1497 hits Total gene families after translated alignment: 3226 Unaligned reads after translated alignment: 3.2689280092 % Computing gene families ... Computing pathways abundance and coverage ... Output files created: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCW6_genefamilies.tsv /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCW6_pathabundance.tsv /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCW6_pathcoverage.tsv Stderr: 2017-07-18 19:04:34,402 LoggerReporter log_event INFO: task 29, humann____CSM5MCW6 : completed successfully 2017-07-18 19:04:34,402 LoggerReporter log_event INFO: task 36, humann_regroup_UniRef2EC____CSM5MCW6 : ready and waiting for resources 2017-07-18 19:04:34,403 LoggerReporter log_event INFO: task 36, humann_regroup_UniRef2EC____CSM5MCW6 : starting to run 2017-07-18 19:04:34,403 LoggerReporter task_command INFO: Executing with shell: humann_regroup_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCW6_genefamilies.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5MCW6_ecs.tsv --groups uniref90_level4ec 2017-07-18 19:04:35,140 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCW6_genefamilies.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCW6_genefamilies.tsv as stratified output, e.g. ['UniRef90_R6JGY4', 'g__Bacteroides.s__Bacteroides_ovatus'] Loading mapping file from: /home/ljmciver/.local/lib/python2.7/site-packages/humann/data/misc/map_level4ec_uniref90.txt.gz Original Feature Count: 3227; Grouped 1+ times: 660 (20.5%); Grouped 2+ times: 3 (0.1%) 2017-07-18 19:04:35,140 LoggerReporter log_event INFO: task 36, humann_regroup_UniRef2EC____CSM5MCW6 : completed successfully 2017-07-18 19:04:35,141 LoggerReporter log_event INFO: task 51, humann_renorm_ecs_relab____CSM5MCW6 : ready and waiting for resources 2017-07-18 19:04:35,141 LoggerReporter log_event INFO: task 51, humann_renorm_ecs_relab____CSM5MCW6 : starting to run 2017-07-18 19:04:35,141 LoggerReporter task_command INFO: Executing with shell: humann_renorm_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5MCW6_ecs.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/ecs/CSM5MCW6_ecs_relab.tsv --units relab --special n 2017-07-18 19:04:35,314 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5MCW6_ecs.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5MCW6_ecs.tsv as stratified output, e.g. ['UNGROUPED', 'g__Bacteroides.s__Bacteroides_caccae'] Excluding special feature: UNMAPPED Excluding special feature: UNGROUPED Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_caccae Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_cellulosilyticus Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_dorei Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_finegoldii Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_fragilis Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_ovatus Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_thetaiotaomicron Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_vulgatus Excluding special feature: UNGROUPED|g__Bifidobacterium.s__Bifidobacterium_longum Excluding special feature: UNGROUPED|g__Blautia.s__Ruminococcus_obeum Excluding special feature: UNGROUPED|g__Blautia.s__Ruminococcus_torques Excluding special feature: UNGROUPED|g__Dorea.s__Dorea_formicigenerans Excluding special feature: UNGROUPED|g__Faecalibacterium.s__Faecalibacterium_prausnitzii Excluding special feature: UNGROUPED|g__Parabacteroides.s__Parabacteroides_distasonis Excluding special feature: UNGROUPED|g__Streptococcus.s__Streptococcus_parasanguinis Excluding special feature: UNGROUPED|g__Streptococcus.s__Streptococcus_salivarius Excluding special feature: UNGROUPED|unclassified 2017-07-18 19:04:35,315 LoggerReporter log_event INFO: task 51, humann_renorm_ecs_relab____CSM5MCW6 : completed successfully 2017-07-18 19:04:35,315 LoggerReporter log_event INFO: task 45, humann_renorm_genes_relab____CSM5MCW6 : ready and waiting for resources 2017-07-18 19:04:35,315 LoggerReporter log_event INFO: task 45, humann_renorm_genes_relab____CSM5MCW6 : starting to run 2017-07-18 19:04:35,315 LoggerReporter task_command INFO: Executing with shell: humann_renorm_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCW6_genefamilies.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/genes/CSM5MCW6_genefamilies_relab.tsv --units relab --special n 2017-07-18 19:04:35,538 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCW6_genefamilies.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCW6_genefamilies.tsv as stratified output, e.g. ['UniRef90_R6JGY4', 'g__Bacteroides.s__Bacteroides_ovatus'] Excluding special feature: UNMAPPED 2017-07-18 19:04:35,538 LoggerReporter log_event INFO: task 45, humann_renorm_genes_relab____CSM5MCW6 : completed successfully 2017-07-18 19:04:35,539 LoggerReporter log_event INFO: task 57, humann_renorm_pathways_relab____CSM5MCW6 : ready and waiting for resources 2017-07-18 19:04:35,539 LoggerReporter log_event INFO: task 57, humann_renorm_pathways_relab____CSM5MCW6 : starting to run 2017-07-18 19:04:35,539 LoggerReporter task_command INFO: Executing with shell: humann_renorm_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCW6_pathabundance.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/pathways/CSM5MCW6_pathabundance_relab.tsv --units relab --special n 2017-07-18 19:04:35,725 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCW6_pathabundance.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCW6_pathabundance.tsv as stratified output, e.g. ['UNINTEGRATED', 'g__Faecalibacterium.s__Faecalibacterium_prausnitzii'] Excluding special feature: UNMAPPED Excluding special feature: UNINTEGRATED Excluding special feature: UNINTEGRATED|g__Faecalibacterium.s__Faecalibacterium_prausnitzii Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_caccae Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_cellulosilyticus Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_dorei Excluding special feature: UNINTEGRATED|g__Parabacteroides.s__Parabacteroides_distasonis Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_vulgatus Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_ovatus Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_fragilis Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_thetaiotaomicron Excluding special feature: UNINTEGRATED|g__Streptococcus.s__Streptococcus_salivarius Excluding special feature: UNINTEGRATED|g__Blautia.s__Ruminococcus_obeum Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_finegoldii Excluding special feature: UNINTEGRATED|g__Bifidobacterium.s__Bifidobacterium_longum Excluding special feature: UNINTEGRATED|g__Dorea.s__Dorea_formicigenerans Excluding special feature: UNINTEGRATED|unclassified Excluding special feature: UNINTEGRATED|g__Blautia.s__Ruminococcus_torques 2017-07-18 19:04:35,726 LoggerReporter log_event INFO: task 57, humann_renorm_pathways_relab____CSM5MCW6 : completed successfully 2017-07-18 19:04:35,727 LoggerReporter log_event INFO: task 0, kneaddata____CSM5MCWC : ready and waiting for resources 2017-07-18 19:04:35,728 LoggerReporter log_event INFO: task 0, kneaddata____CSM5MCWC : starting to run 2017-07-18 19:04:35,877 LoggerReporter task_command INFO: Tracked executable version: kneaddata v0.6.1 2017-07-18 19:04:35,877 LoggerReporter task_command INFO: Executing with shell: kneaddata --input /work/code/biobakery_workflows/examples/tutorial/input/CSM5MCWC.fastq.gz --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main --threads 1 --output-prefix CSM5MCWC --reference-db /work/code/biobakery_workflows/examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/ --serial 2017-07-18 19:04:39,658 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Decompressing gzipped file ... Initial number of reads ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/decompressed_BIM9k1_CSM5MCWC.fastq ): 61076 Running Trimmomatic ... Total reads after trimming ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCWC.trimmed.fastq ): 61013 Decontaminating ... Running bowtie2 ... Running bowtie2 ... Total reads after removing those found in reference database ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCWC_Homo_sapiens_demo_bowtie2_clean.fastq ): 60948 Total reads after merging results from multiple databases ( /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCWC.fastq ): 60854 Final output file created: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCWC.fastq Stderr: 2017-07-18 19:04:39,659 LoggerReporter log_event INFO: task 0, kneaddata____CSM5MCWC : completed successfully 2017-07-18 19:04:39,660 LoggerReporter log_event INFO: task 13, kneaddata_read_count_table : ready and waiting for resources 2017-07-18 19:04:39,660 LoggerReporter log_event INFO: task 13, kneaddata_read_count_table : starting to run 2017-07-18 19:04:39,660 LoggerReporter task_command INFO: Executing with shell: kneaddata_read_count_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/merged/kneaddata_read_count_table.tsv 2017-07-18 19:04:39,857 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Reading log: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCVN.log Reading log: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCW6.log Reading log: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCWC.log Reading log: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5FZ4M.log Reading log: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCUO.log Reading log: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCVL.log Read count table written: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/merged/kneaddata_read_count_table.tsv Stderr: 2017-07-18 19:04:39,858 LoggerReporter log_event INFO: task 13, kneaddata_read_count_table : completed successfully 2017-07-18 19:04:39,858 LoggerReporter log_event INFO: task 14, metaphlan____CSM5MCWC : ready and waiting for resources 2017-07-18 19:04:39,858 LoggerReporter log_event INFO: task 14, metaphlan____CSM5MCWC : starting to run 2017-07-18 19:04:39,937 LoggerReporter task_command INFO: Tracked executable version: MetaPhlAn version 3 2017-07-18 19:04:39,938 LoggerReporter task_command INFO: Executing with shell: metaphlan /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCWC.fastq --input_type fastq --output_file /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main/CSM5MCWC_taxonomic_profile.tsv --samout /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main/CSM5MCWC_bowtie2.sam --nproc 1 --no_map --tmp_dir /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main 2017-07-18 19:05:34,179 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: 2017-07-18 19:05:34,179 LoggerReporter log_event INFO: task 14, metaphlan____CSM5MCWC : completed successfully 2017-07-18 19:20:54,554 LoggerReporter log_event INFO: task 21, metaphlan_join_taxonomic_profiles : ready and waiting for resources 2017-07-18 19:20:54,554 LoggerReporter log_event INFO: task 21, metaphlan_join_taxonomic_profiles : starting to run 2017-07-18 19:20:54,554 LoggerReporter task_command INFO: Executing with shell: humann_join_tables --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/merged/metaphlan_taxonomic_profiles.tsv --file_name taxonomic_profile 2017-07-18 19:20:54,733 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Gene table created: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/merged/metaphlan_taxonomic_profiles.tsv Stderr: 2017-07-18 19:20:54,734 LoggerReporter log_event INFO: task 21, metaphlan_join_taxonomic_profiles : completed successfully 2017-07-18 19:20:54,734 LoggerReporter log_event INFO: task 22, metaphlan_count_species : ready and waiting for resources 2017-07-18 19:20:54,734 LoggerReporter log_event INFO: task 22, metaphlan_count_species : starting to run 2017-07-18 19:20:54,734 LoggerReporter task_command INFO: Executing with shell: count_features.py --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/merged/metaphlan_taxonomic_profiles.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/merged/metaphlan_species_counts_table.tsv --include s__ --filter t__ --reduce-sample-name 2017-07-18 19:20:54,893 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: 2017-07-18 19:20:54,894 LoggerReporter log_event INFO: task 22, metaphlan_count_species : completed successfully 2017-07-18 19:20:54,894 LoggerReporter log_event INFO: task 23, humann____CSM5MCWC : ready and waiting for resources 2017-07-18 19:20:54,894 LoggerReporter log_event INFO: task 23, humann____CSM5MCWC : starting to run 2017-07-18 19:20:55,101 LoggerReporter task_command INFO: Tracked executable version: humann v3 2017-07-18 19:20:55,101 LoggerReporter task_command INFO: Executing with shell: humann --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/kneaddata/main/CSM5MCWC.fastq --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main --o-log /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCWC.log --threads 1 --taxonomic-profile /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/metaphlan/main/CSM5MCWC_taxonomic_profile.tsv 2017-07-18 19:25:32,287 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Output files will be written to: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main Found g__Streptococcus.s__Streptococcus_vestibularis : 11.30% of mapped reads Found g__Lactobacillus.s__Lactobacillus_salivarius : 10.91% of mapped reads Found g__Klebsiella.s__Klebsiella_pneumoniae : 9.65% of mapped reads Found g__Escherichia.s__Escherichia_coli : 8.50% of mapped reads Found g__Haemophilus.s__Haemophilus_parainfluenzae : 8.11% of mapped reads Found g__Streptococcus.s__Streptococcus_parasanguinis : 8.07% of mapped reads Found g__Bacteroides.s__Bacteroides_caccae : 5.83% of mapped reads Found g__Bifidobacterium.s__Bifidobacterium_dentium : 5.40% of mapped reads Found g__Bacteroides.s__Bacteroides_thetaiotaomicron : 5.29% of mapped reads Found g__Bacteroides.s__Bacteroides_vulgatus : 4.74% of mapped reads Found g__Bacteroides.s__Bacteroides_ovatus : 4.70% of mapped reads Found g__Streptococcus.s__Streptococcus_salivarius : 4.50% of mapped reads Found g__Bifidobacterium.s__Bifidobacterium_longum : 3.07% of mapped reads Found g__Faecalibacterium.s__Faecalibacterium_prausnitzii : 2.94% of mapped reads Found g__Blautia.s__Ruminococcus_torques : 2.58% of mapped reads Found g__Bacteroides.s__Bacteroides_dorei : 2.15% of mapped reads Found g__Streptococcus.s__Streptococcus_anginosus : 2.00% of mapped reads Found g__Bacteroides.s__Bacteroides_fragilis : 0.16% of mapped reads Found g__Bacteroides.s__Bacteroides_xylanisolvens : 0.11% of mapped reads Total species selected from prescreen: 19 Selected species explain 100.00% of predicted community composition Creating custom ChocoPhlAn database ........ Running bowtie2-build ........ Running bowtie2 ........ Total bugs from nucleotide alignment: 14 g__Streptococcus.s__Streptococcus_salivarius: 1722 hits g__Bifidobacterium.s__Bifidobacterium_dentium: 1031 hits g__Klebsiella.s__Klebsiella_pneumoniae: 2564 hits g__Bacteroides.s__Bacteroides_caccae: 4134 hits g__Blautia.s__Ruminococcus_torques: 18 hits g__Bacteroides.s__Bacteroides_ovatus: 15773 hits g__Bacteroides.s__Bacteroides_fragilis: 66 hits g__Bacteroides.s__Bacteroides_vulgatus: 17909 hits g__Bacteroides.s__Bacteroides_thetaiotaomicron: 2548 hits g__Bacteroides.s__Bacteroides_xylanisolvens: 1272 hits g__Faecalibacterium.s__Faecalibacterium_prausnitzii: 921 hits g__Streptococcus.s__Streptococcus_parasanguinis: 1113 hits g__Bifidobacterium.s__Bifidobacterium_longum: 476 hits g__Bacteroides.s__Bacteroides_dorei: 2401 hits Total gene families from nucleotide alignment: 2315 Unaligned reads after nucleotide alignment: 14.6350281000 % Running diamond ........ Aligning to reference database: uniref90_demo_prots.dmnd Total bugs after translated alignment: 15 g__Streptococcus.s__Streptococcus_salivarius: 1722 hits g__Bifidobacterium.s__Bifidobacterium_dentium: 1031 hits g__Klebsiella.s__Klebsiella_pneumoniae: 2564 hits g__Bacteroides.s__Bacteroides_caccae: 4134 hits g__Blautia.s__Ruminococcus_torques: 18 hits g__Bacteroides.s__Bacteroides_ovatus: 15773 hits g__Bacteroides.s__Bacteroides_fragilis: 66 hits unclassified: 11009 hits g__Bacteroides.s__Bacteroides_vulgatus: 17909 hits g__Bacteroides.s__Bacteroides_thetaiotaomicron: 2548 hits g__Bacteroides.s__Bacteroides_xylanisolvens: 1272 hits g__Faecalibacterium.s__Faecalibacterium_prausnitzii: 921 hits g__Streptococcus.s__Streptococcus_parasanguinis: 1113 hits g__Bifidobacterium.s__Bifidobacterium_longum: 476 hits g__Bacteroides.s__Bacteroides_dorei: 2401 hits Total gene families after translated alignment: 2895 Unaligned reads after translated alignment: 6.1047753640 % Computing gene families ... Computing pathways abundance and coverage ... Output files created: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCWC_genefamilies.tsv /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCWC_pathabundance.tsv /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCWC_pathcoverage.tsv Stderr: 2017-07-18 19:25:32,288 LoggerReporter log_event INFO: task 23, humann____CSM5MCWC : completed successfully 2017-07-18 19:25:32,289 LoggerReporter log_event INFO: task 37, humann_join_tables_genefamilies : ready and waiting for resources 2017-07-18 19:25:32,289 LoggerReporter log_event INFO: task 37, humann_join_tables_genefamilies : starting to run 2017-07-18 19:25:32,289 LoggerReporter task_command INFO: Executing with shell: humann_join_tables --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/merged/genefamilies.tsv --file_name genefamilies 2017-07-18 19:25:32,544 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Gene table created: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/merged/genefamilies.tsv Stderr: 2017-07-18 19:25:32,545 LoggerReporter log_event INFO: task 37, humann_join_tables_genefamilies : completed successfully 2017-07-18 19:25:32,545 LoggerReporter log_event INFO: task 39, humann_join_tables_pathabundance : ready and waiting for resources 2017-07-18 19:25:32,546 LoggerReporter log_event INFO: task 39, humann_join_tables_pathabundance : starting to run 2017-07-18 19:25:32,546 LoggerReporter task_command INFO: Executing with shell: humann_join_tables --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/merged/pathabundance.tsv --file_name pathabundance 2017-07-18 19:25:32,772 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Gene table created: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/merged/pathabundance.tsv Stderr: 2017-07-18 19:25:32,773 LoggerReporter log_event INFO: task 39, humann_join_tables_pathabundance : completed successfully 2017-07-18 19:25:32,773 LoggerReporter log_event INFO: task 40, humann_renorm_genes_relab____CSM5MCWC : ready and waiting for resources 2017-07-18 19:25:32,774 LoggerReporter log_event INFO: task 40, humann_renorm_genes_relab____CSM5MCWC : starting to run 2017-07-18 19:25:32,774 LoggerReporter task_command INFO: Executing with shell: humann_renorm_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCWC_genefamilies.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/genes/CSM5MCWC_genefamilies_relab.tsv --units relab --special n 2017-07-18 19:25:33,046 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCWC_genefamilies.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCWC_genefamilies.tsv as stratified output, e.g. ['UniRef90_R6JGY4', 'g__Bacteroides.s__Bacteroides_ovatus'] Excluding special feature: UNMAPPED 2017-07-18 19:25:33,047 LoggerReporter log_event INFO: task 40, humann_renorm_genes_relab____CSM5MCWC : completed successfully 2017-07-18 19:25:33,047 LoggerReporter log_event INFO: task 58, humann_join_tables_genes_relab : ready and waiting for resources 2017-07-18 19:25:33,048 LoggerReporter log_event INFO: task 58, humann_join_tables_genes_relab : starting to run 2017-07-18 19:25:33,048 LoggerReporter task_command INFO: Executing with shell: humann_join_tables --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/genes --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/merged/genefamilies_relab.tsv 2017-07-18 19:25:33,506 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Gene table created: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/merged/genefamilies_relab.tsv Stderr: 2017-07-18 19:25:33,507 LoggerReporter log_event INFO: task 58, humann_join_tables_genes_relab : completed successfully 2017-07-18 19:25:33,507 LoggerReporter log_event INFO: task 61, humann_count_features_genes : ready and waiting for resources 2017-07-18 19:25:33,508 LoggerReporter log_event INFO: task 61, humann_count_features_genes : starting to run 2017-07-18 19:25:33,508 LoggerReporter task_command INFO: Executing with shell: count_features.py --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/merged/genefamilies_relab.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/counts/humann_genefamilies_relab_counts.tsv --reduce-sample-name --ignore-un-features --ignore-stratification 2017-07-18 19:25:33,709 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: 2017-07-18 19:25:33,710 LoggerReporter log_event INFO: task 61, humann_count_features_genes : completed successfully 2017-07-18 19:25:33,710 LoggerReporter log_event INFO: task 52, humann_renorm_pathways_relab____CSM5MCWC : ready and waiting for resources 2017-07-18 19:25:33,711 LoggerReporter log_event INFO: task 52, humann_renorm_pathways_relab____CSM5MCWC : starting to run 2017-07-18 19:25:33,711 LoggerReporter task_command INFO: Executing with shell: humann_renorm_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCWC_pathabundance.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/pathways/CSM5MCWC_pathabundance_relab.tsv --units relab --special n 2017-07-18 19:25:33,905 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCWC_pathabundance.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCWC_pathabundance.tsv as stratified output, e.g. ['UNINTEGRATED', 'g__Bacteroides.s__Bacteroides_vulgatus'] Excluding special feature: UNMAPPED Excluding special feature: UNINTEGRATED Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_vulgatus Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_ovatus Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_caccae Excluding special feature: UNINTEGRATED|g__Klebsiella.s__Klebsiella_pneumoniae Excluding special feature: UNINTEGRATED|g__Streptococcus.s__Streptococcus_salivarius Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_thetaiotaomicron Excluding special feature: UNINTEGRATED|g__Streptococcus.s__Streptococcus_parasanguinis Excluding special feature: UNINTEGRATED|g__Bifidobacterium.s__Bifidobacterium_dentium Excluding special feature: UNINTEGRATED|g__Faecalibacterium.s__Faecalibacterium_prausnitzii Excluding special feature: UNINTEGRATED|unclassified Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_dorei Excluding special feature: UNINTEGRATED|g__Bacteroides.s__Bacteroides_xylanisolvens Excluding special feature: UNINTEGRATED|g__Bifidobacterium.s__Bifidobacterium_longum 2017-07-18 19:25:33,905 LoggerReporter log_event INFO: task 52, humann_renorm_pathways_relab____CSM5MCWC : completed successfully 2017-07-18 19:25:33,906 LoggerReporter log_event INFO: task 60, humann_join_tables_pathways_relab : ready and waiting for resources 2017-07-18 19:25:33,906 LoggerReporter log_event INFO: task 60, humann_join_tables_pathways_relab : starting to run 2017-07-18 19:25:33,906 LoggerReporter task_command INFO: Executing with shell: humann_join_tables --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/pathways --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/merged/pathabundance_relab.tsv 2017-07-18 19:25:34,095 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Gene table created: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/merged/pathabundance_relab.tsv Stderr: 2017-07-18 19:25:34,095 LoggerReporter log_event INFO: task 60, humann_join_tables_pathways_relab : completed successfully 2017-07-18 19:25:34,096 LoggerReporter log_event INFO: task 63, humann_count_features_pathways : ready and waiting for resources 2017-07-18 19:25:34,096 LoggerReporter log_event INFO: task 63, humann_count_features_pathways : starting to run 2017-07-18 19:25:34,096 LoggerReporter task_command INFO: Executing with shell: count_features.py --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/merged/pathabundance_relab.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/counts/humann_pathabundance_relab_counts.tsv --reduce-sample-name --ignore-un-features --ignore-stratification 2017-07-18 19:25:34,268 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: 2017-07-18 19:25:34,269 LoggerReporter log_event INFO: task 63, humann_count_features_pathways : completed successfully 2017-07-18 19:25:34,269 LoggerReporter log_event INFO: task 30, humann_count_alignments_species : ready and waiting for resources 2017-07-18 19:25:34,270 LoggerReporter log_event INFO: task 30, humann_count_alignments_species : starting to run 2017-07-18 19:25:34,270 LoggerReporter task_command INFO: Executing with shell: get_counts_from_humann_logs.py --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/counts/humann_read_and_species_count_table.tsv 2017-07-18 19:25:34,512 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Read table written to file: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/counts/humann_read_and_species_count_table.tsv Stderr: 2017-07-18 19:25:34,513 LoggerReporter log_event INFO: task 30, humann_count_alignments_species : completed successfully 2017-07-18 19:25:34,513 LoggerReporter log_event INFO: task 31, humann_regroup_UniRef2EC____CSM5MCWC : ready and waiting for resources 2017-07-18 19:25:34,513 LoggerReporter log_event INFO: task 31, humann_regroup_UniRef2EC____CSM5MCWC : starting to run 2017-07-18 19:25:34,514 LoggerReporter task_command INFO: Executing with shell: humann_regroup_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCWC_genefamilies.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5MCWC_ecs.tsv --groups uniref90_level4ec 2017-07-18 19:25:35,228 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCWC_genefamilies.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/main/CSM5MCWC_genefamilies.tsv as stratified output, e.g. ['UniRef90_R6JGY4', 'g__Bacteroides.s__Bacteroides_ovatus'] Loading mapping file from: /home/ljmciver/.local/lib/python2.7/site-packages/humann/data/misc/map_level4ec_uniref90.txt.gz Original Feature Count: 2896; Grouped 1+ times: 959 (33.1%); Grouped 2+ times: 7 (0.2%) 2017-07-18 19:25:35,228 LoggerReporter log_event INFO: task 31, humann_regroup_UniRef2EC____CSM5MCWC : completed successfully 2017-07-18 19:25:35,229 LoggerReporter log_event INFO: task 46, humann_renorm_ecs_relab____CSM5MCWC : ready and waiting for resources 2017-07-18 19:25:35,229 LoggerReporter log_event INFO: task 46, humann_renorm_ecs_relab____CSM5MCWC : starting to run 2017-07-18 19:25:35,229 LoggerReporter task_command INFO: Executing with shell: humann_renorm_table --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5MCWC_ecs.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/ecs/CSM5MCWC_ecs_relab.tsv --units relab --special n 2017-07-18 19:25:35,384 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: Loading table from: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5MCWC_ecs.tsv Treating /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped/CSM5MCWC_ecs.tsv as stratified output, e.g. ['UNGROUPED', 'g__Bacteroides.s__Bacteroides_caccae'] Excluding special feature: UNMAPPED Excluding special feature: UNGROUPED Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_caccae Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_dorei Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_fragilis Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_ovatus Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_thetaiotaomicron Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_vulgatus Excluding special feature: UNGROUPED|g__Bacteroides.s__Bacteroides_xylanisolvens Excluding special feature: UNGROUPED|g__Bifidobacterium.s__Bifidobacterium_dentium Excluding special feature: UNGROUPED|g__Bifidobacterium.s__Bifidobacterium_longum Excluding special feature: UNGROUPED|g__Blautia.s__Ruminococcus_torques Excluding special feature: UNGROUPED|g__Faecalibacterium.s__Faecalibacterium_prausnitzii Excluding special feature: UNGROUPED|g__Klebsiella.s__Klebsiella_pneumoniae Excluding special feature: UNGROUPED|g__Streptococcus.s__Streptococcus_parasanguinis Excluding special feature: UNGROUPED|g__Streptococcus.s__Streptococcus_salivarius Excluding special feature: UNGROUPED|unclassified 2017-07-18 19:25:35,384 LoggerReporter log_event INFO: task 46, humann_renorm_ecs_relab____CSM5MCWC : completed successfully 2017-07-18 19:25:35,384 LoggerReporter log_event INFO: task 59, humann_join_tables_ecs_relab : ready and waiting for resources 2017-07-18 19:25:35,385 LoggerReporter log_event INFO: task 59, humann_join_tables_ecs_relab : starting to run 2017-07-18 19:25:35,385 LoggerReporter task_command INFO: Executing with shell: humann_join_tables --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/relab/ecs --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/merged/ecs_relab.tsv 2017-07-18 19:25:35,566 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Gene table created: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/merged/ecs_relab.tsv Stderr: 2017-07-18 19:25:35,566 LoggerReporter log_event INFO: task 59, humann_join_tables_ecs_relab : completed successfully 2017-07-18 19:25:35,567 LoggerReporter log_event INFO: task 62, humann_count_features_ecs : ready and waiting for resources 2017-07-18 19:25:35,567 LoggerReporter log_event INFO: task 62, humann_count_features_ecs : starting to run 2017-07-18 19:25:35,567 LoggerReporter task_command INFO: Executing with shell: count_features.py --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/merged/ecs_relab.tsv --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/counts/humann_ecs_relab_counts.tsv --reduce-sample-name --ignore-un-features --ignore-stratification 2017-07-18 19:25:35,733 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Stderr: 2017-07-18 19:25:35,733 LoggerReporter log_event INFO: task 62, humann_count_features_ecs : completed successfully 2017-07-18 19:25:35,734 LoggerReporter log_event INFO: task 64, humann_merge_feature_counts : ready and waiting for resources 2017-07-18 19:25:35,734 LoggerReporter log_event INFO: task 64, humann_merge_feature_counts : starting to run 2017-07-18 19:25:35,734 LoggerReporter task_command INFO: Executing with shell: humann_join_tables --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/counts --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/counts/humann_feature_counts.tsv --file_name _relab_counts.tsv 2017-07-18 19:25:35,887 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Gene table created: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/counts/humann_feature_counts.tsv Stderr: 2017-07-18 19:25:35,887 LoggerReporter log_event INFO: task 64, humann_merge_feature_counts : completed successfully 2017-07-18 19:25:35,888 LoggerReporter log_event INFO: task 38, humann_join_tables_ecs : ready and waiting for resources 2017-07-18 19:25:35,888 LoggerReporter log_event INFO: task 38, humann_join_tables_ecs : starting to run 2017-07-18 19:25:35,888 LoggerReporter task_command INFO: Executing with shell: humann_join_tables --input /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/regrouped --output /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/merged/ecs.tsv --file_name ecs 2017-07-18 19:25:36,081 anadama2.helpers actually_sh INFO: Execution complete. Stdout: Gene table created: /work/code/biobakery_workflows/biobakery_workflows_tutorial_output/humann/merged/ecs.tsv Stderr: 2017-07-18 19:25:36,081 LoggerReporter log_event INFO: task 38, humann_join_tables_ecs : completed successfully 2017-07-18 19:25:36,081 LoggerReporter finished INFO: AnADAMA run finished.