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October 9, 2014 16:16
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| Selecting previously unselected package libxpp3-java. | |
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| Setting up maven (3.0.5-1) ... | |
| update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode | |
| vagrant@vagrant-ubuntu-trusty-64:~/gatk$ mvn | |
| [INFO] Scanning for projects... | |
| [INFO] ------------------------------------------------------------------------ | |
| [INFO] Reactor Build Order: | |
| [INFO] | |
| [INFO] GATK Root | |
| [INFO] GATK Aggregator | |
| [INFO] GATK GSALib | |
| [INFO] GATK Utils | |
| [INFO] GATK Engine | |
| [INFO] GATK Tools Public | |
| [INFO] External Example | |
| [INFO] GATK Queue | |
| [INFO] GATK Queue Extensions Generator | |
| [INFO] GATK Queue Extensions Public | |
| [INFO] GATK Aggregator Public | |
| [INFO] ------------------------------------------------------------------------ | |
| [INFO] Reactor Summary: | |
| [INFO] | |
| [INFO] GATK Root ......................................... SKIPPED | |
| [INFO] GATK Aggregator ................................... SKIPPED | |
| [INFO] GATK GSALib ....................................... SKIPPED | |
| [INFO] GATK Utils ........................................ SKIPPED | |
| [INFO] GATK Engine ....................................... SKIPPED | |
| [INFO] GATK Tools Public ................................. SKIPPED | |
| [INFO] External Example .................................. SKIPPED | |
| [INFO] GATK Queue ........................................ SKIPPED | |
| [INFO] GATK Queue Extensions Generator ................... SKIPPED | |
| [INFO] GATK Queue Extensions Public ...................... SKIPPED | |
| [INFO] GATK Aggregator Public ............................ SKIPPED | |
| [INFO] ------------------------------------------------------------------------ | |
| [INFO] BUILD FAILURE | |
| [INFO] ------------------------------------------------------------------------ | |
| [INFO] Total time: 1.098s | |
| [INFO] Finished at: Fri Oct 03 18:28:07 UTC 2014 | |
| [INFO] Final Memory: 7M/17M | |
| [INFO] ------------------------------------------------------------------------ | |
| [ERROR] No goals have been specified for this build. You must specify a valid lifecycle phase or a goal in the format <plugin-prefix>:<goal> or <plugin-group-id>:<plugin-artifact-id>[:<plugin-version>]:<goal>. Available lifecycle phases are: validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy, pre-site, site, post-site, site-deploy, pre-clean, clean, post-clean. -> [Help 1] | |
| [ERROR] | |
| [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. | |
| [ERROR] Re-run Maven using the -X switch to enable full debug logging. | |
| [ERROR] | |
| [ERROR] For more information about the errors and possible solutions, please read the following articles: | |
| [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/NoGoalSpecifiedException | |
| vagrant@vagrant-ubuntu-trusty-64:~/gatk$ pwd | |
| /home/vagrant/gatk | |
| vagrant@vagrant-ubuntu-trusty-64:~/gatk$ cd ../ | |
| .ant/ .cache/ .continuum/ gatk/ Library/ .ssh/ | |
| bcbio-nextgen/ .config/ .cpanm/ gatk2/ .m2/ tmp/ | |
| vagrant@vagrant-ubuntu-trusty-64:~/gatk$ cd ~/ | |
| .ant/ .cache/ .continuum/ gatk/ Library/ .ssh/ | |
| bcbio-nextgen/ .config/ .cpanm/ gatk2/ .m2/ tmp/ | |
| vagrant@vagrant-ubuntu-trusty-64:~/gatk$ cd ~/tmp/ | |
| vagrant@vagrant-ubuntu-trusty-64:~/tmp$ ls | |
| bcbio_nextgen_install.py | |
| vagrant@vagrant-ubuntu-trusty-64:~/tmp$ cd ../bcbio-nextgen/ | |
| vagrant@vagrant-ubuntu-trusty-64:~/bcbio-nextgen$ ls | |
| bcbio config Dockerfile docs HISTORY.md LICENSE.txt MANIFEST.in README.rst requirements.txt scripts setup.py tests TODO.md | |
| vagrant@vagrant-ubuntu-trusty-64:~/bcbio-nextgen$ cd tests/ | |
| vagrant@vagrant-ubuntu-trusty-64:~/bcbio-nextgen/tests$ ./run_tests.sh | |
| Check for the presence of runs in an Illumina SampleSheet. ... ok | |
| Convert CSV Illumina SampleSheet to YAML. ... ok | |
| Test variant calling with GATK pipeline. ... [2014-10-03 18:57] Using input YAML configuration: /home/vagrant/bcbio-nextgen/tests/data/automated/run_info-variantcall.yaml | |
| [2014-10-03 18:57] Checking sample YAML configuration: /home/vagrant/bcbio-nextgen/tests/data/automated/run_info-variantcall.yaml | |
| [2014-10-03 18:57] Testing minimum versions of installed programs | |
| [2014-10-03 18:57] Resource requests: novoalign, sambamba, samtools; memory: 2.0, 2.0; cores: 16, 1, 16 | |
| [2014-10-03 18:57] Configuring 1 jobs to run, using 1 cores each with 2.2g of memory reserved for each job | |
| [2014-10-03 18:57] Timing: alignment preparation | |
| [2014-10-03 18:57] multiprocessing: prep_align_inputs | |
| [2014-10-03 18:57] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 18:57] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 18:57] bgzip input file | |
| [2014-10-03 18:57] bgzip input file | |
| [2014-10-03 18:57] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 18:57] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 18:57] Index input with grabix: 7_100326_FC6107FAAXX_1_fastq.txt.gz | |
| [2014-10-03 18:57] Index input with grabix: 7_100326_FC6107FAAXX_2_fastq.txt.gz | |
| [2014-10-03 18:57] Timing: alignment | |
| [2014-10-03 18:57] multiprocessing: process_alignment | |
| [2014-10-03 18:57] Aligning lane 7_100326_FC6107FAAXX with novoalign aligner | |
| [2014-10-03 18:57] Novoalign: Test1 | |
| [2014-10-03 18:57] samblaster: Version 0.1.20 | |
| [2014-10-03 18:57] samblaster: Inputting from stdin | |
| [2014-10-03 18:57] samblaster: Outputting to stdout | |
| [2014-10-03 18:57] samblaster: Opening /dev/fd/62 for write. | |
| [2014-10-03 18:57] samblaster: Opening /dev/fd/63 for write. | |
| [2014-10-03 18:57] Command line argument ignored: -c option is only available in licensed versions. at '-c' | |
| [2014-10-03 18:57] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 18:57] Command line argument ignored: -k option is only available in licensed versions. at '-k' | |
| [2014-10-03 18:57] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 18:57] # novoalign (V3.02.02 - Build Feb 4 2014 @ 15:23:48 - A short read aligner with qualities. | |
| [2014-10-03 18:57] # (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd. | |
| [2014-10-03 18:57] # License file not found. | |
| [2014-10-03 18:57] # Licensed for evaluation, educational, and not-for-profit use only. | |
| [2014-10-03 18:57] # novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 18:57] # Starting at Fri Oct 3 18:57:08 2014 | |
| [2014-10-03 18:57] # Interpreting input files as Sanger FASTQ. | |
| [2014-10-03 18:57] # Index Build Version: 2.7 | |
| [2014-10-03 18:57] # Hash length: 6 | |
| [2014-10-03 18:57] # Step size: 1 | |
| [2014-10-03 18:57] samblaster: Loaded 2 header sequence entries. | |
| [2014-10-03 18:57] # Paired Reads: 9000 | |
| [2014-10-03 18:57] # Pairs Aligned: 8889 | |
| [2014-10-03 18:57] # Read Sequences: 18000 | |
| [2014-10-03 18:57] # Aligned: 17874 | |
| [2014-10-03 18:57] # Unique Alignment: 17874 | |
| [2014-10-03 18:57] # Gapped Alignment: 67 | |
| [2014-10-03 18:57] # Quality Filter: 126 | |
| [2014-10-03 18:57] # Homopolymer Filter: 0 | |
| [2014-10-03 18:57] # Elapsed Time: 2.508 (secs.) | |
| [2014-10-03 18:57] # CPU Time: 2.36 (secs.) | |
| [2014-10-03 18:57] # Fragment Length Distribution | |
| [2014-10-03 18:57] # From To Count | |
| [2014-10-03 18:57] # 60 74 9 | |
| [2014-10-03 18:57] # 75 89 197 | |
| [2014-10-03 18:57] # 90 104 300 | |
| [2014-10-03 18:57] # 105 119 628 | |
| [2014-10-03 18:57] # 120 134 1584 | |
| [2014-10-03 18:57] # 135 149 1604 | |
| [2014-10-03 18:57] # 150 164 1419 | |
| [2014-10-03 18:57] # 165 179 1258 | |
| [2014-10-03 18:57] # 180 194 967 | |
| [2014-10-03 18:57] # 195 209 677 | |
| [2014-10-03 18:57] # 210 224 223 | |
| [2014-10-03 18:57] # 225 239 21 | |
| [2014-10-03 18:57] # 240 254 2 | |
| [2014-10-03 18:57] # Mean 153, Std Dev 31.1 | |
| [2014-10-03 18:57] # Done at Fri Oct 3 18:57:11 2014 | |
| [2014-10-03 18:57] samblaster: Output 0 discordant read pairs to /dev/fd/62 | |
| [2014-10-03 18:57] samblaster: Output 0 split reads to /dev/fd/63 | |
| [2014-10-03 18:57] samblaster: Marked 97 of 9000 (1.08%) read ids as duplicates using 1332k memory in 0.030S CPU seconds and 3S wall time. | |
| [2014-10-03 18:57] Index BAM file: 7_100326_FC6107FAAXX-sort-1_36000.bam | |
| [2014-10-03 18:57] Index BAM file: 7_100326_FC6107FAAXX-sort-1_36000-sr.bam | |
| [2014-10-03 18:57] Index BAM file: 7_100326_FC6107FAAXX-sort-1_36000-disc.bam | |
| [2014-10-03 18:57] Aligning lane 7_100326_FC6107FAAXX with novoalign aligner | |
| [2014-10-03 18:57] Novoalign: Test1 | |
| [2014-10-03 18:57] samblaster: Version 0.1.20 | |
| [2014-10-03 18:57] samblaster: Inputting from stdin | |
| [2014-10-03 18:57] samblaster: Outputting to stdout | |
| [2014-10-03 18:57] samblaster: Opening /dev/fd/62 for write. | |
| [2014-10-03 18:57] samblaster: Opening /dev/fd/63 for write. | |
| [2014-10-03 18:57] Command line argument ignored: -c option is only available in licensed versions. at '-c' | |
| [2014-10-03 18:57] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 18:57] Command line argument ignored: -k option is only available in licensed versions. at '-k' | |
| [2014-10-03 18:57] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 18:57] # novoalign (V3.02.02 - Build Feb 4 2014 @ 15:23:48 - A short read aligner with qualities. | |
| [2014-10-03 18:57] # (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd. | |
| [2014-10-03 18:57] # License file not found. | |
| [2014-10-03 18:57] # Licensed for evaluation, educational, and not-for-profit use only. | |
| [2014-10-03 18:57] # novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 18:57] # Starting at Fri Oct 3 18:57:11 2014 | |
| [2014-10-03 18:57] # Interpreting input files as Sanger FASTQ. | |
| [2014-10-03 18:57] # Index Build Version: 2.7 | |
| [2014-10-03 18:57] # Hash length: 6 | |
| [2014-10-03 18:57] # Step size: 1 | |
| [2014-10-03 18:57] samblaster: Loaded 2 header sequence entries. | |
| [2014-10-03 18:57] # Paired Reads: 9000 | |
| [2014-10-03 18:57] # Pairs Aligned: 8899 | |
| [2014-10-03 18:57] # Read Sequences: 18000 | |
| [2014-10-03 18:57] # Aligned: 17888 | |
| [2014-10-03 18:57] # Unique Alignment: 17888 | |
| [2014-10-03 18:57] # Gapped Alignment: 48 | |
| [2014-10-03 18:57] # Quality Filter: 112 | |
| [2014-10-03 18:57] # Homopolymer Filter: 0 | |
| [2014-10-03 18:57] # Elapsed Time: 2.519 (secs.) | |
| [2014-10-03 18:57] # CPU Time: 2.38 (secs.) | |
| [2014-10-03 18:57] # Fragment Length Distribution | |
| [2014-10-03 18:57] # From To Count | |
| [2014-10-03 18:57] # 60 74 5 | |
| [2014-10-03 18:57] # 75 89 195 | |
| [2014-10-03 18:57] # 90 104 308 | |
| [2014-10-03 18:57] # 105 119 669 | |
| [2014-10-03 18:57] # 120 134 1511 | |
| [2014-10-03 18:57] # 135 149 1656 | |
| [2014-10-03 18:57] # 150 164 1379 | |
| [2014-10-03 18:57] # 165 179 1207 | |
| [2014-10-03 18:57] # 180 194 1020 | |
| [2014-10-03 18:57] # 195 209 692 | |
| [2014-10-03 18:57] # 210 224 231 | |
| [2014-10-03 18:57] # 225 239 19 | |
| [2014-10-03 18:57] # 240 254 4 | |
| [2014-10-03 18:57] # 255 269 2 | |
| [2014-10-03 18:57] # 270 284 1 | |
| [2014-10-03 18:57] # Mean 153, Std Dev 31.4 | |
| [2014-10-03 18:57] # Done at Fri Oct 3 18:57:14 2014 | |
| [2014-10-03 18:57] samblaster: Output 1 discordant read pairs to /dev/fd/62 | |
| [2014-10-03 18:57] samblaster: Output 0 split reads to /dev/fd/63 | |
| [2014-10-03 18:57] samblaster: Marked 105 of 9000 (1.17%) read ids as duplicates using 1328k memory in 0.048S CPU seconds and 3S wall time. | |
| [2014-10-03 18:57] Index BAM file: 7_100326_FC6107FAAXX-sort-36000_71999.bam | |
| [2014-10-03 18:57] Index BAM file: 7_100326_FC6107FAAXX-sort-36000_71999-sr.bam | |
| [2014-10-03 18:57] Index BAM file: 7_100326_FC6107FAAXX-sort-36000_71999-disc.bam | |
| [2014-10-03 18:57] Aligning lane 7_100326_FC6107FAAXX with novoalign aligner | |
| [2014-10-03 18:57] Novoalign: Test1 | |
| [2014-10-03 18:57] samblaster: Version 0.1.20 | |
| [2014-10-03 18:57] samblaster: Inputting from stdin | |
| [2014-10-03 18:57] samblaster: Outputting to stdout | |
| [2014-10-03 18:57] samblaster: Opening /dev/fd/62 for write. | |
| [2014-10-03 18:57] samblaster: Opening /dev/fd/63 for write. | |
| [2014-10-03 18:57] Command line argument ignored: -c option is only available in licensed versions. at '-c' | |
| [2014-10-03 18:57] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 18:57] Command line argument ignored: -k option is only available in licensed versions. at '-k' | |
| [2014-10-03 18:57] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 18:57] # novoalign (V3.02.02 - Build Feb 4 2014 @ 15:23:48 - A short read aligner with qualities. | |
| [2014-10-03 18:57] # (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd. | |
| [2014-10-03 18:57] # License file not found. | |
| [2014-10-03 18:57] # Licensed for evaluation, educational, and not-for-profit use only. | |
| [2014-10-03 18:57] # novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 18:57] # Starting at Fri Oct 3 18:57:14 2014 | |
| [2014-10-03 18:57] # Interpreting input files as Sanger FASTQ. | |
| [2014-10-03 18:57] # Index Build Version: 2.7 | |
| [2014-10-03 18:57] # Hash length: 6 | |
| [2014-10-03 18:57] # Step size: 1 | |
| [2014-10-03 18:57] samblaster: Loaded 2 header sequence entries. | |
| [2014-10-03 18:57] # Paired Reads: 9000 | |
| [2014-10-03 18:57] # Pairs Aligned: 8881 | |
| [2014-10-03 18:57] # Read Sequences: 18000 | |
| [2014-10-03 18:57] # Aligned: 17872 | |
| [2014-10-03 18:57] # Unique Alignment: 17872 | |
| [2014-10-03 18:57] # Gapped Alignment: 53 | |
| [2014-10-03 18:57] # Quality Filter: 128 | |
| [2014-10-03 18:57] # Homopolymer Filter: 0 | |
| [2014-10-03 18:57] # Elapsed Time: 2.544 (secs.) | |
| [2014-10-03 18:57] # CPU Time: 2.42 (secs.) | |
| [2014-10-03 18:57] # Fragment Length Distribution | |
| [2014-10-03 18:57] # From To Count | |
| [2014-10-03 18:57] # 60 74 5 | |
| [2014-10-03 18:57] # 75 89 194 | |
| [2014-10-03 18:57] # 90 104 304 | |
| [2014-10-03 18:57] # 105 119 695 | |
| [2014-10-03 18:57] # 120 134 1547 | |
| [2014-10-03 18:57] # 135 149 1598 | |
| [2014-10-03 18:57] # 150 164 1399 | |
| [2014-10-03 18:57] # 165 179 1229 | |
| [2014-10-03 18:57] # 180 194 1010 | |
| [2014-10-03 18:57] # 195 209 669 | |
| [2014-10-03 18:57] # 210 224 202 | |
| [2014-10-03 18:57] # 225 239 24 | |
| [2014-10-03 18:57] # 240 254 2 | |
| [2014-10-03 18:57] # 255 269 2 | |
| [2014-10-03 18:57] # 270 284 1 | |
| [2014-10-03 18:57] # Mean 152, Std Dev 31.2 | |
| [2014-10-03 18:57] # Done at Fri Oct 3 18:57:16 2014 | |
| [2014-10-03 18:57] samblaster: Output 0 discordant read pairs to /dev/fd/62 | |
| [2014-10-03 18:57] samblaster: Output 0 split reads to /dev/fd/63 | |
| [2014-10-03 18:57] samblaster: Marked 105 of 9000 (1.17%) read ids as duplicates using 1332k memory in 0.037S CPU seconds and 2S wall time. | |
| [2014-10-03 18:57] Index BAM file: 7_100326_FC6107FAAXX-sort-72000_107999.bam | |
| [2014-10-03 18:57] Index BAM file: 7_100326_FC6107FAAXX-sort-72000_107999-sr.bam | |
| [2014-10-03 18:57] Index BAM file: 7_100326_FC6107FAAXX-sort-72000_107999-disc.bam | |
| [2014-10-03 18:57] Aligning lane 7_100326_FC6107FAAXX with novoalign aligner | |
| [2014-10-03 18:57] Novoalign: Test1 | |
| [2014-10-03 18:57] samblaster: Version 0.1.20 | |
| [2014-10-03 18:57] samblaster: Inputting from stdin | |
| [2014-10-03 18:57] samblaster: Outputting to stdout | |
| [2014-10-03 18:57] samblaster: Opening /dev/fd/62 for write. | |
| [2014-10-03 18:57] samblaster: Opening /dev/fd/63 for write. | |
| [2014-10-03 18:57] Command line argument ignored: -c option is only available in licensed versions. at '-c' | |
| [2014-10-03 18:57] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 18:57] Command line argument ignored: -k option is only available in licensed versions. at '-k' | |
| [2014-10-03 18:57] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 18:57] # novoalign (V3.02.02 - Build Feb 4 2014 @ 15:23:48 - A short read aligner with qualities. | |
| [2014-10-03 18:57] # (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd. | |
| [2014-10-03 18:57] # License file not found. | |
| [2014-10-03 18:57] # Licensed for evaluation, educational, and not-for-profit use only. | |
| [2014-10-03 18:57] # novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 18:57] # Starting at Fri Oct 3 18:57:17 2014 | |
| [2014-10-03 18:57] # Interpreting input files as Sanger FASTQ. | |
| [2014-10-03 18:57] # Index Build Version: 2.7 | |
| [2014-10-03 18:57] # Hash length: 6 | |
| [2014-10-03 18:57] # Step size: 1 | |
| [2014-10-03 18:57] samblaster: Loaded 2 header sequence entries. | |
| [2014-10-03 18:57] # Paired Reads: 9000 | |
| [2014-10-03 18:57] # Pairs Aligned: 8907 | |
| [2014-10-03 18:57] # Read Sequences: 18000 | |
| [2014-10-03 18:57] # Aligned: 17899 | |
| [2014-10-03 18:57] # Unique Alignment: 17899 | |
| [2014-10-03 18:57] # Gapped Alignment: 58 | |
| [2014-10-03 18:57] # Quality Filter: 101 | |
| [2014-10-03 18:57] # Homopolymer Filter: 0 | |
| [2014-10-03 18:57] # Elapsed Time: 2.526 (secs.) | |
| [2014-10-03 18:57] # CPU Time: 2.39 (secs.) | |
| [2014-10-03 18:57] # Fragment Length Distribution | |
| [2014-10-03 18:57] # From To Count | |
| [2014-10-03 18:57] # 60 74 5 | |
| [2014-10-03 18:57] # 75 89 203 | |
| [2014-10-03 18:57] # 90 104 351 | |
| [2014-10-03 18:57] # 105 119 680 | |
| [2014-10-03 18:57] # 120 134 1579 | |
| [2014-10-03 18:57] # 135 149 1551 | |
| [2014-10-03 18:57] # 150 164 1378 | |
| [2014-10-03 18:57] # 165 179 1255 | |
| [2014-10-03 18:57] # 180 194 984 | |
| [2014-10-03 18:57] # 195 209 684 | |
| [2014-10-03 18:57] # 210 224 203 | |
| [2014-10-03 18:57] # 225 239 27 | |
| [2014-10-03 18:57] # 240 254 6 | |
| [2014-10-03 18:57] # 255 269 1 | |
| [2014-10-03 18:57] # Mean 152, Std Dev 31.6 | |
| [2014-10-03 18:57] # Done at Fri Oct 3 18:57:19 2014 | |
| [2014-10-03 18:57] samblaster: Output 0 discordant read pairs to /dev/fd/62 | |
| [2014-10-03 18:57] samblaster: Output 0 split reads to /dev/fd/63 | |
| [2014-10-03 18:57] samblaster: Marked 106 of 9000 (1.18%) read ids as duplicates using 1332k memory in 0.009S CPU seconds and 2S wall time. | |
| [2014-10-03 18:57] Index BAM file: 7_100326_FC6107FAAXX-sort-108000_143999.bam | |
| [2014-10-03 18:57] Index BAM file: 7_100326_FC6107FAAXX-sort-108000_143999-sr.bam | |
| [2014-10-03 18:57] Index BAM file: 7_100326_FC6107FAAXX-sort-108000_143999-disc.bam | |
| [2014-10-03 18:57] Aligning lane 7_100326_FC6107FAAXX with novoalign aligner | |
| [2014-10-03 18:57] Novoalign: Test1 | |
| [2014-10-03 18:57] samblaster: Version 0.1.20 | |
| [2014-10-03 18:57] samblaster: Inputting from stdin | |
| [2014-10-03 18:57] samblaster: Outputting to stdout | |
| [2014-10-03 18:57] samblaster: Opening /dev/fd/62 for write. | |
| [2014-10-03 18:57] samblaster: Opening /dev/fd/63 for write. | |
| [2014-10-03 18:57] Command line argument ignored: -c option is only available in licensed versions. at '-c' | |
| [2014-10-03 18:57] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 18:57] Command line argument ignored: -k option is only available in licensed versions. at '-k' | |
| [2014-10-03 18:57] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 18:57] # novoalign (V3.02.02 - Build Feb 4 2014 @ 15:23:48 - A short read aligner with qualities. | |
| [2014-10-03 18:57] # (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd. | |
| [2014-10-03 18:57] # License file not found. | |
| [2014-10-03 18:57] # Licensed for evaluation, educational, and not-for-profit use only. | |
| [2014-10-03 18:57] # novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 18:57] # Starting at Fri Oct 3 18:57:19 2014 | |
| [2014-10-03 18:57] # Interpreting input files as Sanger FASTQ. | |
| [2014-10-03 18:57] # Index Build Version: 2.7 | |
| [2014-10-03 18:57] # Hash length: 6 | |
| [2014-10-03 18:57] # Step size: 1 | |
| [2014-10-03 18:57] samblaster: Loaded 2 header sequence entries. | |
| [2014-10-03 18:57] # Paired Reads: 4164 | |
| [2014-10-03 18:57] # Pairs Aligned: 4099 | |
| [2014-10-03 18:57] # Read Sequences: 8328 | |
| [2014-10-03 18:57] # Aligned: 8231 | |
| [2014-10-03 18:57] # Unique Alignment: 8231 | |
| [2014-10-03 18:57] # Gapped Alignment: 57 | |
| [2014-10-03 18:57] # Quality Filter: 28 | |
| [2014-10-03 18:57] # Homopolymer Filter: 0 | |
| [2014-10-03 18:57] # Elapsed Time: 1.278 (secs.) | |
| [2014-10-03 18:57] # CPU Time: 1.21 (secs.) | |
| [2014-10-03 18:57] # Fragment Length Distribution | |
| [2014-10-03 18:57] # From To Count | |
| [2014-10-03 18:57] # 60 74 2 | |
| [2014-10-03 18:57] # 75 89 84 | |
| [2014-10-03 18:57] # 90 104 151 | |
| [2014-10-03 18:57] # 105 119 311 | |
| [2014-10-03 18:57] # 120 134 693 | |
| [2014-10-03 18:57] # 135 149 757 | |
| [2014-10-03 18:57] # 150 164 667 | |
| [2014-10-03 18:57] # 165 179 544 | |
| [2014-10-03 18:57] # 180 194 426 | |
| [2014-10-03 18:57] # 195 209 310 | |
| [2014-10-03 18:57] # 210 224 112 | |
| [2014-10-03 18:57] # 225 239 16 | |
| [2014-10-03 18:57] # 240 254 14 | |
| [2014-10-03 18:57] # 255 269 1 | |
| [2014-10-03 18:57] # 270 284 1 | |
| [2014-10-03 18:57] # 285 299 1 | |
| [2014-10-03 18:57] # 300 314 3 | |
| [2014-10-03 18:57] # 315 329 0 | |
| [2014-10-03 18:57] # 330 344 1 | |
| [2014-10-03 18:57] # 345 359 0 | |
| [2014-10-03 18:57] # 360 374 0 | |
| [2014-10-03 18:57] # 375 389 1 | |
| [2014-10-03 18:57] # 390 404 0 | |
| [2014-10-03 18:57] # 405 419 0 | |
| [2014-10-03 18:57] # 420 434 0 | |
| [2014-10-03 18:57] # 435 449 0 | |
| [2014-10-03 18:57] # 450 464 0 | |
| [2014-10-03 18:57] # 465 479 0 | |
| [2014-10-03 18:57] # 480 494 0 | |
| [2014-10-03 18:57] # 495 509 1 | |
| [2014-10-03 18:57] # Mean 153, Std Dev 32.9 | |
| [2014-10-03 18:57] # Done at Fri Oct 3 18:57:21 2014 | |
| [2014-10-03 18:57] samblaster: Output 3 discordant read pairs to /dev/fd/62 | |
| [2014-10-03 18:57] samblaster: Output 0 split reads to /dev/fd/63 | |
| [2014-10-03 18:57] samblaster: Marked 31 of 4164 (0.74%) read ids as duplicates using 1332k memory in 0.023S CPU seconds and 2S wall time. | |
| [2014-10-03 18:57] Index BAM file: 7_100326_FC6107FAAXX-sort-144000_160655.bam | |
| [2014-10-03 18:57] Index BAM file: 7_100326_FC6107FAAXX-sort-144000_160655-sr.bam | |
| [2014-10-03 18:57] Index BAM file: 7_100326_FC6107FAAXX-sort-144000_160655-disc.bam | |
| [2014-10-03 18:57] multiprocessing: delayed_bam_merge | |
| [2014-10-03 18:57] Merge bam files to 7_100326_FC6107FAAXX-sort-sr.bam | |
| [2014-10-03 18:57] Index BAM file: 7_100326_FC6107FAAXX-sort-sr.bam | |
| [2014-10-03 18:57] Merge bam files to 7_100326_FC6107FAAXX-sort-disc.bam | |
| [2014-10-03 18:57] Index BAM file: 7_100326_FC6107FAAXX-sort-disc.bam | |
| [2014-10-03 18:57] Merge bam files to 7_100326_FC6107FAAXX-sort.bam | |
| [2014-10-03 18:57] Index BAM file: 7_100326_FC6107FAAXX-sort.bam | |
| [2014-10-03 18:57] Timing: callable regions | |
| [2014-10-03 18:57] multiprocessing: prep_samples | |
| [2014-10-03 18:57] Prepare cleaned BED file : Test1 | |
| [2014-10-03 18:57] bgzip variant_regions-variantcall.bed | |
| [2014-10-03 18:57] tabix index variant_regions-variantcall.bed.gz | |
| [2014-10-03 18:57] Prepare merged BED file : Test1 | |
| [2014-10-03 18:57] bgzip variant_regions-variantcall-merged.bed | |
| [2014-10-03 18:57] tabix index variant_regions-variantcall-merged.bed.gz | |
| [2014-10-03 18:57] multiprocessing: postprocess_alignment | |
| [2014-10-03 18:57] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 18:57] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 18:57] multiprocessing: calc_callable_loci | |
| [2014-10-03 18:57] bedtools genomecov: chrM : 7_100326_FC6107FAAXX-sort.bam | |
| [2014-10-03 18:57] bedtools genomecov: chr22 : 7_100326_FC6107FAAXX-sort.bam | |
| [2014-10-03 18:57] multiprocessing: combine_bed | |
| [2014-10-03 18:57] Recalibrating ['', 'Test1'] with GATK | |
| [2014-10-03 18:57] GATK: BaseRecalibrator | |
| [2014-10-03 18:57] INFO 18:57:24,392 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:57] INFO 18:57:24,395 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 18:57] INFO 18:57:24,396 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:57] INFO 18:57:24,396 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:57] INFO 18:57:24,400 HelpFormatter - Program Args: -T BaseRecalibrator -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/tx/tmprNuYHl/7_100326_FC6107FAAXX-sort.grp -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.bam -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --knownSites /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-variantcall.bed --interval_set_rule INTERSECTION -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment | |
| [2014-10-03 18:57] INFO 18:57:24,404 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:57] INFO 18:57:24,405 HelpFormatter - Date/Time: 2014/10/03 18:57:24 | |
| [2014-10-03 18:57] INFO 18:57:24,406 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:57] INFO 18:57:24,406 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:57] INFO 18:57:24,981 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:57] INFO 18:57:25,092 GenomeAnalysisEngine - Downsampling Settings: No downsampling | |
| [2014-10-03 18:57] INFO 18:57:25,100 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 18:57] INFO 18:57:25,107 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 18:57] INFO 18:57:25,151 IntervalUtils - Processing 5650 bp from intervals | |
| [2014-10-03 18:57] WARN 18:57:25,153 IndexDictionaryUtils - Track knownSites doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 18:57] INFO 18:57:25,216 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 18:57] INFO 18:57:25,235 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:57] INFO 18:57:25,236 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:57] INFO 18:57:25,237 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 18:57] INFO 18:57:25,238 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime | |
| [2014-10-03 18:57] INFO 18:57:25,268 BaseRecalibrator - The covariates being used here: | |
| [2014-10-03 18:57] INFO 18:57:25,272 BaseRecalibrator - ReadGroupCovariate | |
| [2014-10-03 18:57] INFO 18:57:25,274 BaseRecalibrator - QualityScoreCovariate | |
| [2014-10-03 18:57] INFO 18:57:25,275 BaseRecalibrator - ContextCovariate | |
| [2014-10-03 18:57] INFO 18:57:25,276 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3 | |
| [2014-10-03 18:57] INFO 18:57:25,277 BaseRecalibrator - CycleCovariate | |
| [2014-10-03 18:57] INFO 18:57:25,279 ReadShardBalancer$1 - Loading BAM index data | |
| [2014-10-03 18:57] INFO 18:57:25,281 ReadShardBalancer$1 - Done loading BAM index data | |
| [2014-10-03 18:57] INFO 18:57:26,384 ReadShardBalancer$1 - Loading BAM index data | |
| [2014-10-03 18:57] INFO 18:57:26,385 ReadShardBalancer$1 - Done loading BAM index data | |
| [2014-10-03 18:57] INFO 18:57:31,142 BaseRecalibrator - Calculating quantized quality scores... | |
| [2014-10-03 18:57] INFO 18:57:31,195 BaseRecalibrator - Writing recalibration report... | |
| [2014-10-03 18:57] INFO 18:57:32,283 BaseRecalibrator - ...done! | |
| [2014-10-03 18:57] INFO 18:57:32,285 BaseRecalibrator - BaseRecalibrator was able to recalibrate 78308 reads | |
| [2014-10-03 18:57] INFO 18:57:32,287 ProgressMeter - done 78308.0 7.0 s 90.0 s 87.2% 8.0 s 1.0 s | |
| [2014-10-03 18:57] INFO 18:57:32,288 ProgressMeter - Total runtime 7.05 secs, 0.12 min, 0.00 hours | |
| [2014-10-03 18:57] INFO 18:57:32,289 MicroScheduler - 1258 reads were filtered out during the traversal out of approximately 79566 total reads (1.58%) | |
| [2014-10-03 18:57] INFO 18:57:32,289 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 18:57] INFO 18:57:32,296 MicroScheduler - -> 866 reads (1.09% of total) failing DuplicateReadFilter | |
| [2014-10-03 18:57] INFO 18:57:32,301 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter | |
| [2014-10-03 18:57] INFO 18:57:32,302 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 18:57] INFO 18:57:32,303 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter | |
| [2014-10-03 18:57] INFO 18:57:32,303 MicroScheduler - -> 392 reads (0.49% of total) failing MappingQualityZeroFilter | |
| [2014-10-03 18:57] INFO 18:57:32,304 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 18:57] INFO 18:57:32,304 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter | |
| [2014-10-03 18:57] INFO 18:57:38,771 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 18:57] multiprocessing: combine_sample_regions | |
| [2014-10-03 18:57] Identified 2 parallel analysis blocks | |
| Block sizes: | |
| min: 5000 | |
| 5%: 5479.75 | |
| 25%: 7398.75 | |
| median: 9797.5 | |
| 75%: 12196.25 | |
| 95%: 14115.25 | |
| 99%: 14499.05 | |
| max: 14595 | |
| Between block sizes: | |
| [] | |
| [2014-10-03 18:57] Timing: coverage | |
| [2014-10-03 18:57] Resource requests: freebayes, gatk, picard; memory: 2.0, 3.5, 3.5; cores: 1, 1, 1 | |
| [2014-10-03 18:57] Configuring 1 jobs to run, using 1 cores each with 3.8g of memory reserved for each job | |
| [2014-10-03 18:57] Timing: alignment post-processing | |
| [2014-10-03 18:57] multiprocessing: piped_bamprep | |
| [2014-10-03 18:57] GATK pre-alignment ('chrM', 0, 5000) : Test1 | |
| [2014-10-03 18:57] INFO 18:57:40,777 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 18:57] INFO 18:57:40,780 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53 | |
| [2014-10-03 18:57] INFO 18:57:40,781 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:57] INFO 18:57:40,781 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:57] INFO 18:57:40,784 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T PrintReads -L chrM:1-5000 -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.bam --downsample_to_coverage 10000 -BQSR /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.grp -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chrM/tx/tmps6ZodR/7_100326_FC6107FAAXX-sort-chrM_0_5000-prep-prealign.bam | |
| [2014-10-03 18:57] INFO 18:57:40,787 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:57] INFO 18:57:40,788 HelpFormatter - Date/Time: 2014/10/03 18:57:40 | |
| [2014-10-03 18:57] INFO 18:57:40,789 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 18:57] INFO 18:57:40,789 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 18:57] INFO 18:57:41,259 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:57] INFO 18:57:41,305 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000 | |
| [2014-10-03 18:57] INFO 18:57:41,311 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 18:57] INFO 18:57:41,320 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 18:57] INFO 18:57:41,329 IntervalUtils - Processing 5000 bp from intervals | |
| [2014-10-03 18:57] INFO 18:57:41,384 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 18:57] INFO 18:57:41,401 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:57] INFO 18:57:41,402 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:57] INFO 18:57:41,403 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 18:57] INFO 18:57:41,404 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime | |
| [2014-10-03 18:57] INFO 18:57:41,408 ReadShardBalancer$1 - Loading BAM index data | |
| [2014-10-03 18:57] INFO 18:57:41,409 ReadShardBalancer$1 - Done loading BAM index data | |
| [2014-10-03 18:57] INFO 18:57:43,934 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@74dee4ec | |
| [2014-10-03 18:57] INFO 18:57:43,939 ProgressMeter - done 79879.0 2.0 s 31.0 s 100.0% 2.0 s 0.0 s | |
| [2014-10-03 18:57] INFO 18:57:43,941 ProgressMeter - Total runtime 2.54 secs, 0.04 min, 0.00 hours | |
| [2014-10-03 18:57] INFO 18:57:43,943 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 79879 total reads (0.00%) | |
| [2014-10-03 18:57] INFO 18:57:43,944 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 18:57] INFO 18:57:43,945 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 18:57] INFO 18:57:43,946 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 18:57] Index BAM file: 7_100326_FC6107FAAXX-sort-chrM_0_5000-prep-prealign.bam | |
| [2014-10-03 18:57] GATK RealignerTargetCreator: 7_100326_FC6107FAAXX-sort-chrM_0_5000-prep-prealign.bam chrM:1-5000 | |
| [2014-10-03 18:57] GATK: RealignerTargetCreator | |
| [2014-10-03 18:57] INFO 18:57:45,935 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:57] INFO 18:57:45,938 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 18:57] INFO 18:57:45,938 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:57] INFO 18:57:45,939 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:57] INFO 18:57:45,942 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chrM/7_100326_FC6107FAAXX-sort-chrM_0_5000-prep-prealign.bam -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chrM/tx/tmpAQPmru/7_100326_FC6107FAAXX-sort-chrM_0_5000-prep-prealign-realign.intervals -l INFO -L chrM:1-5000 --interval_set_rule INTERSECTION --known /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment | |
| [2014-10-03 18:57] INFO 18:57:45,945 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:57] INFO 18:57:45,946 HelpFormatter - Date/Time: 2014/10/03 18:57:45 | |
| [2014-10-03 18:57] INFO 18:57:45,947 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:57] INFO 18:57:45,947 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:57] INFO 18:57:46,395 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:57] INFO 18:57:46,448 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:57] INFO 18:57:46,454 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 18:57] INFO 18:57:46,461 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 18:57] INFO 18:57:46,497 IntervalUtils - Processing 5000 bp from intervals | |
| [2014-10-03 18:57] WARN 18:57:46,500 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 18:57] INFO 18:57:46,549 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 18:57] INFO 18:57:46,565 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:57] INFO 18:57:46,566 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:57] INFO 18:57:46,566 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 18:57] INFO 18:57:46,568 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 18:57] INFO 18:57:48,567 ProgressMeter - done 5000.0 2.0 s 6.7 m 98.0% 2.0 s 0.0 s | |
| [2014-10-03 18:57] INFO 18:57:48,571 ProgressMeter - Total runtime 2.01 secs, 0.03 min, 0.00 hours | |
| [2014-10-03 18:57] INFO 18:57:48,572 MicroScheduler - 1274 reads were filtered out during the traversal out of approximately 79879 total reads (1.59%) | |
| [2014-10-03 18:57] INFO 18:57:48,574 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 18:57] INFO 18:57:48,574 MicroScheduler - -> 0 reads (0.00% of total) failing BadMateFilter | |
| [2014-10-03 18:57] INFO 18:57:48,575 MicroScheduler - -> 872 reads (1.09% of total) failing DuplicateReadFilter | |
| [2014-10-03 18:57] INFO 18:57:48,575 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter | |
| [2014-10-03 18:57] INFO 18:57:48,576 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 18:57] INFO 18:57:48,577 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter | |
| [2014-10-03 18:57] INFO 18:57:48,577 MicroScheduler - -> 402 reads (0.50% of total) failing MappingQualityZeroFilter | |
| [2014-10-03 18:57] INFO 18:57:48,578 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 18:57] INFO 18:57:48,579 MicroScheduler - -> 0 reads (0.00% of total) failing Platform454Filter | |
| [2014-10-03 18:57] INFO 18:57:48,579 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter | |
| [2014-10-03 18:57] INFO 18:57:54,903 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 18:57] GATK: realign ('chrM', 0, 5000) : Test1 | |
| [2014-10-03 18:57] INFO 18:57:56,674 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:57] INFO 18:57:56,676 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 18:57] INFO 18:57:56,677 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:57] INFO 18:57:56,677 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:57] INFO 18:57:56,680 HelpFormatter - Program Args: -T IndelRealigner -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chrM/7_100326_FC6107FAAXX-sort-chrM_0_5000-prep-prealign.bam -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -targetIntervals /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chrM/7_100326_FC6107FAAXX-sort-chrM_0_5000-prep-prealign-realign.intervals -L chrM:1-5000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chrM/tx/tmpNh9QZO/7_100326_FC6107FAAXX-sort-chrM_0_5000-prep.bam | |
| [2014-10-03 18:57] INFO 18:57:56,682 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:57] INFO 18:57:56,683 HelpFormatter - Date/Time: 2014/10/03 18:57:56 | |
| [2014-10-03 18:57] INFO 18:57:56,684 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:57] INFO 18:57:56,684 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:57] INFO 18:57:57,223 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:57] INFO 18:57:57,258 GenomeAnalysisEngine - Downsampling Settings: No downsampling | |
| [2014-10-03 18:57] INFO 18:57:57,265 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 18:57] INFO 18:57:57,273 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 18:57] INFO 18:57:57,281 IntervalUtils - Processing 5000 bp from intervals | |
| [2014-10-03 18:57] INFO 18:57:57,330 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 18:57] INFO 18:57:57,343 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:57] INFO 18:57:57,347 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:57] INFO 18:57:57,348 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 18:57] INFO 18:57:57,349 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime | |
| [2014-10-03 18:57] INFO 18:57:57,360 ReadShardBalancer$1 - Loading BAM index data | |
| [2014-10-03 18:57] INFO 18:57:57,361 ReadShardBalancer$1 - Done loading BAM index data | |
| [2014-10-03 18:58] INFO 18:58:01,986 ProgressMeter - done 79879.0 4.0 s 58.0 s 100.0% 4.0 s 0.0 s | |
| [2014-10-03 18:58] INFO 18:58:01,987 ProgressMeter - Total runtime 4.64 secs, 0.08 min, 0.00 hours | |
| [2014-10-03 18:58] INFO 18:58:01,989 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 79879 total reads (0.00%) | |
| [2014-10-03 18:58] INFO 18:58:01,990 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 18:58] INFO 18:58:01,991 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 18:58] INFO 18:58:01,992 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 18:58] INFO 18:58:08,260 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 18:58] Index BAM file: 7_100326_FC6107FAAXX-sort-chrM_0_5000-prep.bam | |
| [2014-10-03 18:58] GATK pre-alignment ('chr22', 0, 14595) : Test1 | |
| [2014-10-03 18:58] INFO 18:58:10,068 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 18:58] INFO 18:58:10,070 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53 | |
| [2014-10-03 18:58] INFO 18:58:10,071 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:58] INFO 18:58:10,071 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:58] INFO 18:58:10,074 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T PrintReads -L chr22:1-14595 -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.bam --downsample_to_coverage 10000 -BQSR /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.grp -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chr22/tx/tmpAPtxz5/7_100326_FC6107FAAXX-sort-chr22_0_14595-prep-prealign.bam | |
| [2014-10-03 18:58] INFO 18:58:10,077 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:58] INFO 18:58:10,078 HelpFormatter - Date/Time: 2014/10/03 18:58:10 | |
| [2014-10-03 18:58] INFO 18:58:10,079 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 18:58] INFO 18:58:10,079 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 18:58] INFO 18:58:10,538 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:58] INFO 18:58:10,581 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000 | |
| [2014-10-03 18:58] INFO 18:58:10,587 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 18:58] INFO 18:58:10,596 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 18:58] INFO 18:58:10,603 IntervalUtils - Processing 14595 bp from intervals | |
| [2014-10-03 18:58] INFO 18:58:10,651 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 18:58] INFO 18:58:10,665 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:58] INFO 18:58:10,668 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:58] INFO 18:58:10,669 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 18:58] INFO 18:58:10,669 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime | |
| [2014-10-03 18:58] INFO 18:58:10,673 ReadShardBalancer$1 - Loading BAM index data | |
| [2014-10-03 18:58] INFO 18:58:10,674 ReadShardBalancer$1 - Done loading BAM index data | |
| [2014-10-03 18:58] INFO 18:58:10,720 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@74dee4ec | |
| [2014-10-03 18:58] INFO 18:58:10,726 ProgressMeter - done 104.0 0.0 s 9.1 m 99.3% 0.0 s 0.0 s | |
| [2014-10-03 18:58] INFO 18:58:10,726 ProgressMeter - Total runtime 0.06 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:58] INFO 18:58:10,729 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 104 total reads (0.00%) | |
| [2014-10-03 18:58] INFO 18:58:10,729 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 18:58] INFO 18:58:10,730 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 18:58] INFO 18:58:10,731 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 18:58] Index BAM file: 7_100326_FC6107FAAXX-sort-chr22_0_14595-prep-prealign.bam | |
| [2014-10-03 18:58] GATK RealignerTargetCreator: 7_100326_FC6107FAAXX-sort-chr22_0_14595-prep-prealign.bam chr22:1-14595 | |
| [2014-10-03 18:58] GATK: RealignerTargetCreator | |
| [2014-10-03 18:58] INFO 18:58:12,517 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:58] INFO 18:58:12,519 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 18:58] INFO 18:58:12,519 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:58] INFO 18:58:12,520 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:58] INFO 18:58:12,522 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chr22/7_100326_FC6107FAAXX-sort-chr22_0_14595-prep-prealign.bam -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chr22/tx/tmpdbB465/7_100326_FC6107FAAXX-sort-chr22_0_14595-prep-prealign-realign.intervals -l INFO -L chr22:1-14595 --interval_set_rule INTERSECTION --known /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment | |
| [2014-10-03 18:58] INFO 18:58:12,525 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:58] INFO 18:58:12,526 HelpFormatter - Date/Time: 2014/10/03 18:58:12 | |
| [2014-10-03 18:58] INFO 18:58:12,526 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:58] INFO 18:58:12,527 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:58] INFO 18:58:12,943 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:58] INFO 18:58:12,989 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:58] INFO 18:58:12,994 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 18:58] INFO 18:58:13,002 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 18:58] INFO 18:58:13,036 IntervalUtils - Processing 14595 bp from intervals | |
| [2014-10-03 18:58] WARN 18:58:13,038 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 18:58] INFO 18:58:13,084 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 18:58] INFO 18:58:13,099 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:58] INFO 18:58:13,100 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:58] INFO 18:58:13,101 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 18:58] INFO 18:58:13,101 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 18:58] INFO 18:58:13,720 ProgressMeter - done 14595.0 0.0 s 42.0 s 99.3% 0.0 s 0.0 s | |
| [2014-10-03 18:58] INFO 18:58:13,725 ProgressMeter - Total runtime 0.62 secs, 0.01 min, 0.00 hours | |
| [2014-10-03 18:58] INFO 18:58:13,727 MicroScheduler - 2 reads were filtered out during the traversal out of approximately 104 total reads (1.92%) | |
| [2014-10-03 18:58] INFO 18:58:13,732 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 18:58] INFO 18:58:13,733 MicroScheduler - -> 0 reads (0.00% of total) failing BadMateFilter | |
| [2014-10-03 18:58] INFO 18:58:13,733 MicroScheduler - -> 2 reads (1.92% of total) failing DuplicateReadFilter | |
| [2014-10-03 18:58] INFO 18:58:13,734 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter | |
| [2014-10-03 18:58] INFO 18:58:13,741 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 18:58] INFO 18:58:13,741 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter | |
| [2014-10-03 18:58] INFO 18:58:13,742 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityZeroFilter | |
| [2014-10-03 18:58] INFO 18:58:13,742 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 18:58] INFO 18:58:13,743 MicroScheduler - -> 0 reads (0.00% of total) failing Platform454Filter | |
| [2014-10-03 18:58] INFO 18:58:13,744 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter | |
| [2014-10-03 18:58] INFO 18:58:20,074 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 18:58] GATK: realign ('chr22', 0, 14595) : Test1 | |
| [2014-10-03 18:58] INFO 18:58:21,872 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:58] INFO 18:58:21,874 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 18:58] INFO 18:58:21,875 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:58] INFO 18:58:21,876 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:58] INFO 18:58:21,879 HelpFormatter - Program Args: -T IndelRealigner -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chr22/7_100326_FC6107FAAXX-sort-chr22_0_14595-prep-prealign.bam -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -targetIntervals /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chr22/7_100326_FC6107FAAXX-sort-chr22_0_14595-prep-prealign-realign.intervals -L chr22:1-14595 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chr22/tx/tmpB_lYyz/7_100326_FC6107FAAXX-sort-chr22_0_14595-prep.bam | |
| [2014-10-03 18:58] INFO 18:58:21,881 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:58] INFO 18:58:21,882 HelpFormatter - Date/Time: 2014/10/03 18:58:21 | |
| [2014-10-03 18:58] INFO 18:58:21,882 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:58] INFO 18:58:21,883 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:58] INFO 18:58:22,419 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:58] INFO 18:58:22,455 GenomeAnalysisEngine - Downsampling Settings: No downsampling | |
| [2014-10-03 18:58] INFO 18:58:22,460 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 18:58] INFO 18:58:22,469 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 18:58] INFO 18:58:22,477 IntervalUtils - Processing 14595 bp from intervals | |
| [2014-10-03 18:58] INFO 18:58:22,528 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 18:58] INFO 18:58:22,543 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:58] INFO 18:58:22,544 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:58] INFO 18:58:22,545 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 18:58] INFO 18:58:22,546 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime | |
| [2014-10-03 18:58] INFO 18:58:22,558 ReadShardBalancer$1 - Loading BAM index data | |
| [2014-10-03 18:58] INFO 18:58:22,559 ReadShardBalancer$1 - Done loading BAM index data | |
| [2014-10-03 18:58] INFO 18:58:22,632 ProgressMeter - done 104.0 0.0 s 14.0 m 99.3% 0.0 s 0.0 s | |
| [2014-10-03 18:58] INFO 18:58:22,633 ProgressMeter - Total runtime 0.09 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:58] INFO 18:58:22,636 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 104 total reads (0.00%) | |
| [2014-10-03 18:58] INFO 18:58:22,636 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 18:58] INFO 18:58:22,637 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 18:58] INFO 18:58:22,637 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 18:58] INFO 18:58:28,913 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 18:58] Index BAM file: 7_100326_FC6107FAAXX-sort-chr22_0_14595-prep.bam | |
| [2014-10-03 18:58] Select unmapped reads | |
| [2014-10-03 18:58] Index BAM file: 7_100326_FC6107FAAXX-sort-nochrom-prep.bam | |
| [2014-10-03 18:58] Select unanalyzed reads | |
| [2014-10-03 18:58] Index BAM file: 7_100326_FC6107FAAXX-sort-noanalysis-prep.bam | |
| [2014-10-03 18:58] Timing: variant calling | |
| [2014-10-03 18:58] multiprocessing: variantcall_sample | |
| [2014-10-03 18:58] GATK: UnifiedGenotyper | |
| [2014-10-03 18:58] INFO 18:58:31,039 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:58] INFO 18:58:31,041 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 18:58] INFO 18:58:31,042 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:58] INFO 18:58:31,043 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:58] INFO 18:58:31,046 HelpFormatter - Program Args: -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --standard_min_confidence_threshold_for_calling 30.0 --standard_min_confidence_threshold_for_emitting 30.0 --downsample_to_coverage 2000 --downsampling_type BY_SAMPLE --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chrM/7_100326_FC6107FAAXX-sort-chrM_0_5000-prep.bam --dbsnp /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/chrM/TestBatch1-chrM_0_5000-raw-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/chrM/tx/tmp6vmxV9/TestBatch1-chrM_0_5000-raw.vcf.gz -ploidy 1 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment | |
| [2014-10-03 18:58] INFO 18:58:31,050 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:58] INFO 18:58:31,051 HelpFormatter - Date/Time: 2014/10/03 18:58:31 | |
| [2014-10-03 18:58] INFO 18:58:31,052 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:58] INFO 18:58:31,054 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:58] INFO 18:58:31,656 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:58] INFO 18:58:31,721 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 2000 | |
| [2014-10-03 18:58] INFO 18:58:31,727 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 18:58] INFO 18:58:31,738 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 18:58] INFO 18:58:31,773 IntervalUtils - Processing 4900 bp from intervals | |
| [2014-10-03 18:58] WARN 18:58:31,776 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 18:58] INFO 18:58:31,825 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 18:58] INFO 18:58:31,841 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:58] INFO 18:58:31,841 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:58] INFO 18:58:31,842 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 18:58] INFO 18:58:31,844 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 18:58] INFO 18:58:32,415 AFCalcFactory - Requested ploidy 1 maxAltAlleles 6 not supported by requested model EXACT_INDEPENDENT looking for an option | |
| [2014-10-03 18:58] INFO 18:58:32,416 AFCalcFactory - Selecting model EXACT_GENERAL_PLOIDY | |
| [2014-10-03 18:58] INFO 18:58:36,991 ProgressMeter - done 4900.0 5.0 s 17.5 m 98.0% 5.0 s 0.0 s | |
| [2014-10-03 18:58] INFO 18:58:36,993 ProgressMeter - Total runtime 5.15 secs, 0.09 min, 0.00 hours | |
| [2014-10-03 18:58] INFO 18:58:36,993 MicroScheduler - 1258 reads were filtered out during the traversal out of approximately 79552 total reads (1.58%) | |
| [2014-10-03 18:58] INFO 18:58:36,994 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 18:58] INFO 18:58:36,995 MicroScheduler - -> 0 reads (0.00% of total) failing BadMateFilter | |
| [2014-10-03 18:58] INFO 18:58:36,996 MicroScheduler - -> 866 reads (1.09% of total) failing DuplicateReadFilter | |
| [2014-10-03 18:58] INFO 18:58:36,996 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter | |
| [2014-10-03 18:58] INFO 18:58:36,997 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 18:58] INFO 18:58:36,997 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter | |
| [2014-10-03 18:58] INFO 18:58:36,998 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 18:58] INFO 18:58:36,999 MicroScheduler - -> 392 reads (0.49% of total) failing UnmappedReadFilter | |
| [2014-10-03 18:58] INFO 18:58:43,293 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 18:58] GATK: UnifiedGenotyper | |
| [2014-10-03 18:58] INFO 18:58:45,134 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:58] INFO 18:58:45,136 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 18:58] INFO 18:58:45,137 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:58] INFO 18:58:45,138 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:58] INFO 18:58:45,140 HelpFormatter - Program Args: -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --standard_min_confidence_threshold_for_calling 30.0 --standard_min_confidence_threshold_for_emitting 30.0 --downsample_to_coverage 2000 --downsampling_type BY_SAMPLE --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chr22/7_100326_FC6107FAAXX-sort-chr22_0_14595-prep.bam --dbsnp /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/chr22/TestBatch1-chr22_0_14595-raw-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/chr22/tx/tmpB6D0nM/TestBatch1-chr22_0_14595-raw.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment | |
| [2014-10-03 18:58] INFO 18:58:45,143 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:58] INFO 18:58:45,144 HelpFormatter - Date/Time: 2014/10/03 18:58:45 | |
| [2014-10-03 18:58] INFO 18:58:45,144 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:58] INFO 18:58:45,145 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:58] INFO 18:58:45,700 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:58] INFO 18:58:45,764 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 2000 | |
| [2014-10-03 18:58] INFO 18:58:45,770 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 18:58] INFO 18:58:45,782 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 18:58] INFO 18:58:45,813 IntervalUtils - Processing 345 bp from intervals | |
| [2014-10-03 18:58] WARN 18:58:45,815 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 18:58] INFO 18:58:45,860 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 18:58] INFO 18:58:45,877 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:58] INFO 18:58:45,877 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:58] INFO 18:58:45,878 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 18:58] INFO 18:58:45,879 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 18:58] INFO 18:58:46,141 ProgressMeter - done 345.0 0.0 s 12.7 m 87.0% 0.0 s 0.0 s | |
| [2014-10-03 18:58] INFO 18:58:46,143 ProgressMeter - Total runtime 0.27 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:58] INFO 18:58:46,144 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 14 total reads (0.00%) | |
| [2014-10-03 18:58] INFO 18:58:46,145 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 18:58] INFO 18:58:46,145 MicroScheduler - -> 0 reads (0.00% of total) failing BadMateFilter | |
| [2014-10-03 18:58] INFO 18:58:46,146 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter | |
| [2014-10-03 18:58] INFO 18:58:46,147 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter | |
| [2014-10-03 18:58] INFO 18:58:46,147 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 18:58] INFO 18:58:46,148 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter | |
| [2014-10-03 18:58] INFO 18:58:46,148 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 18:58] INFO 18:58:46,149 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter | |
| [2014-10-03 18:58] INFO 18:58:52,447 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 18:58] Genotyping with FreeBayes | |
| [2014-10-03 18:58] tabix index TestBatch1-chrM_0_5000-raw.vcf.gz | |
| [2014-10-03 18:58] GATK: VariantAnnotator | |
| [2014-10-03 18:58] INFO 18:58:56,360 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:58] INFO 18:58:56,362 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 18:58] INFO 18:58:56,363 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:58] INFO 18:58:56,363 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:58] INFO 18:58:56,366 HelpFormatter - Program Args: -T VariantAnnotator -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chrM/TestBatch1-chrM_0_5000-raw.vcf.gz --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chrM/tx/tmpSVTEcb/TestBatch1-chrM_0_5000-raw-gatkann.vcf.gz -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chrM/TestBatch1-chrM_0_5000-raw.vcf.gz --dbsnp /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chrM/7_100326_FC6107FAAXX-sort-chrM_0_5000-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality -A DepthPerAlleleBySample -A Coverage --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment | |
| [2014-10-03 18:58] INFO 18:58:56,368 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:58] INFO 18:58:56,369 HelpFormatter - Date/Time: 2014/10/03 18:58:56 | |
| [2014-10-03 18:58] INFO 18:58:56,369 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:58] INFO 18:58:56,370 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:58] INFO 18:58:56,861 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:58] INFO 18:58:56,926 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 | |
| [2014-10-03 18:58] INFO 18:58:56,932 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 18:58] INFO 18:58:56,944 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 18:58] INFO 18:58:57,000 IntervalUtils - Processing 9 bp from intervals | |
| [2014-10-03 18:58] WARN 18:58:57,006 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 18:58] WARN 18:58:57,007 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 18:58] INFO 18:58:57,084 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 18:58] INFO 18:58:57,100 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:58] INFO 18:58:57,102 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:58] INFO 18:58:57,103 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 18:58] INFO 18:58:57,104 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 18:58] INFO 18:58:58,507 VariantAnnotator - Processed 9 loci. | |
| [2014-10-03 18:58] | |
| [2014-10-03 18:58] INFO 18:58:58,516 ProgressMeter - done 45.0 1.0 s 8.7 h 88.9% 1.0 s 0.0 s | |
| [2014-10-03 18:58] INFO 18:58:58,517 ProgressMeter - Total runtime 1.41 secs, 0.02 min, 0.00 hours | |
| [2014-10-03 18:58] INFO 18:58:58,518 MicroScheduler - 45 reads were filtered out during the traversal out of approximately 6560 total reads (0.69%) | |
| [2014-10-03 18:58] INFO 18:58:58,519 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 18:58] INFO 18:58:58,519 MicroScheduler - -> 44 reads (0.67% of total) failing DuplicateReadFilter | |
| [2014-10-03 18:58] INFO 18:58:58,520 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter | |
| [2014-10-03 18:58] INFO 18:58:58,521 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 18:58] INFO 18:58:58,521 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 18:58] INFO 18:58:58,522 MicroScheduler - -> 1 reads (0.02% of total) failing UnmappedReadFilter | |
| [2014-10-03 18:59] INFO 18:59:04,894 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 18:59] Genotyping with FreeBayes | |
| [2014-10-03 18:59] tabix index TestBatch1-chr22_0_14595-raw.vcf.gz | |
| [2014-10-03 18:59] GATK: VariantAnnotator | |
| [2014-10-03 18:59] INFO 18:59:06,780 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:06,783 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 18:59] INFO 18:59:06,783 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:06,784 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:06,786 HelpFormatter - Program Args: -T VariantAnnotator -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chr22/TestBatch1-chr22_0_14595-raw.vcf.gz --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chr22/tx/tmpBj5Bbk/TestBatch1-chr22_0_14595-raw-gatkann.vcf.gz -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chr22/TestBatch1-chr22_0_14595-raw.vcf.gz --dbsnp /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chr22/7_100326_FC6107FAAXX-sort-chr22_0_14595-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality -A DepthPerAlleleBySample -A Coverage --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment | |
| [2014-10-03 18:59] INFO 18:59:06,789 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:06,790 HelpFormatter - Date/Time: 2014/10/03 18:59:06 | |
| [2014-10-03 18:59] INFO 18:59:06,790 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:06,791 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:07,305 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:07,371 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 | |
| [2014-10-03 18:59] INFO 18:59:07,376 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 18:59] INFO 18:59:07,386 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 18:59] INFO 18:59:07,439 IntervalUtils - Processing 3 bp from intervals | |
| [2014-10-03 18:59] WARN 18:59:07,446 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 18:59] WARN 18:59:07,447 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 18:59] INFO 18:59:07,518 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 18:59] INFO 18:59:07,536 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:07,537 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:07,539 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 18:59] INFO 18:59:07,539 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 18:59] INFO 18:59:07,723 VariantAnnotator - Processed 3 loci. | |
| [2014-10-03 18:59] | |
| [2014-10-03 18:59] INFO 18:59:07,733 ProgressMeter - done 6.0 0.0 s 9.1 h 66.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:07,734 ProgressMeter - Total runtime 0.20 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:07,735 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 9 total reads (0.00%) | |
| [2014-10-03 18:59] INFO 18:59:07,735 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 18:59] INFO 18:59:07,736 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter | |
| [2014-10-03 18:59] INFO 18:59:07,737 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter | |
| [2014-10-03 18:59] INFO 18:59:07,737 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 18:59] INFO 18:59:07,738 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 18:59] INFO 18:59:07,739 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter | |
| [2014-10-03 18:59] INFO 18:59:13,996 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 18:59] multiprocessing: concat_variant_files | |
| [2014-10-03 18:59] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 18:59] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 18:59] Concat variant files | |
| [2014-10-03 18:59] INFO 18:59:15,307 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:15,309 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants | |
| [2014-10-03 18:59] INFO 18:59:15,315 HelpFormatter - Program Args: -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -V /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/TestBatch1-files.list -out /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/tx/tmpftnBDD/TestBatch1.vcf.gz -assumeSorted | |
| [2014-10-03 18:59] INFO 18:59:15,321 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:15,321 HelpFormatter - Date/Time: 2014/10/03 18:59:15 | |
| [2014-10-03 18:59] INFO 18:59:15,323 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:15,323 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 18:59] .. | |
| [2014-10-03 18:59] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 18:59] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 18:59] Concat variant files | |
| [2014-10-03 18:59] INFO 18:59:16,860 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:16,862 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants | |
| [2014-10-03 18:59] INFO 18:59:16,865 HelpFormatter - Program Args: -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -V /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/TestBatch1-files.list -out /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/tx/tmpn5bwGv/TestBatch1.vcf.gz -assumeSorted | |
| [2014-10-03 18:59] INFO 18:59:16,868 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:16,873 HelpFormatter - Date/Time: 2014/10/03 18:59:16 | |
| [2014-10-03 18:59] INFO 18:59:16,874 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:16,874 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 18:59] .. | |
| [2014-10-03 18:59] Resource requests: bamtools, bcbio_variation, fastqc, gatk, gemini, qsignature, samtools, snpeff; memory: 2.5, 3.5, 2.0, 2.0, 6.0; cores: 1, 1, 1, 1, 16, 1, 16, 1 | |
| [2014-10-03 18:59] Configuring 1 jobs to run, using 1 cores each with 6.2g of memory reserved for each job | |
| [2014-10-03 18:59] Timing: joint squaring off/backfilling | |
| [2014-10-03 18:59] Timing: variant post-processing | |
| [2014-10-03 18:59] multiprocessing: postprocess_variants | |
| [2014-10-03 18:59] Finalizing variant calls: Test1, gatk | |
| [2014-10-03 18:59] Calculating variation effects for Test1, gatk | |
| [2014-10-03 18:59] snpEff effects : Test1 | |
| [2014-10-03 18:59] | |
| [2014-10-03 18:59] WARNINGS: Some warning were detected | |
| [2014-10-03 18:59] Warning type Number of warnings | |
| [2014-10-03 18:59] WARNING_TRANSCRIPT_INCOMPLETE 19 | |
| [2014-10-03 18:59] WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS 9 | |
| [2014-10-03 18:59] | |
| [2014-10-03 18:59] | |
| [2014-10-03 18:59] tabix index TestBatch1-effects.vcf.gz | |
| [2014-10-03 18:59] Filtering for Test1, gatk | |
| [2014-10-03 18:59] bgzip TestBatch1-effects-ploidyfix.vcf | |
| [2014-10-03 18:59] tabix index TestBatch1-effects-ploidyfix.vcf.gz | |
| [2014-10-03 18:59] Subset to SNPs and indels | |
| [2014-10-03 18:59] tabix index TestBatch1-effects-ploidyfix-snp.vcf.gz | |
| [2014-10-03 18:59] Subset to SNPs and indels | |
| [2014-10-03 18:59] tabix index TestBatch1-effects-ploidyfix-indel.vcf.gz | |
| [2014-10-03 18:59] Hard filtering /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/TestBatch1-effects-ploidyfix-snp.vcf.gz with QD < 2.0 || MQ < 40.0 || FS > 60.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || HaplotypeScore > 13.0 : Test1 | |
| [2014-10-03 18:59] tabix index TestBatch1-effects-ploidyfix-snp-filterSNP.vcf.gz | |
| [2014-10-03 18:59] tabix index TestBatch1-effects-ploidyfix-indel-filterINDEL.vcf.gz | |
| [2014-10-03 18:59] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 18:59] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 18:59] Combine variant files | |
| [2014-10-03 18:59] INFO 18:59:20,112 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:20,115 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53 | |
| [2014-10-03 18:59] INFO 18:59:20,115 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:20,116 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:20,118 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/tx/tmpcsgenl/TestBatch1-effects-ploidyfix-combined.vcf.gz --variant:v0 /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/TestBatch1-effects-ploidyfix-snp-filterSNP.vcf.gz --variant:v1 /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/TestBatch1-effects-ploidyfix-indel-filterINDEL.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-variantcall.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 18:59] INFO 18:59:20,120 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:20,121 HelpFormatter - Date/Time: 2014/10/03 18:59:20 | |
| [2014-10-03 18:59] INFO 18:59:20,122 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:20,122 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:20,612 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:20,661 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:20,707 IntervalUtils - Processing 5650 bp from intervals | |
| [2014-10-03 18:59] WARN 18:59:20,710 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 18:59] WARN 18:59:20,711 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 18:59] INFO 18:59:20,757 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:20,758 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:20,758 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:20,759 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 18:59] INFO 18:59:20,760 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 18:59] INFO 18:59:20,860 ProgressMeter - done 10.0 0.0 s 2.8 h 89.8% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:20,861 ProgressMeter - Total runtime 0.10 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] Remove stray NON_REF gVCF information from VCF output : Test1 | |
| [2014-10-03 18:59] tabix index TestBatch1-effects-ploidyfix-combined-gatkclean.vcf.gz | |
| [2014-10-03 18:59] Finalizing variant calls: Test1, freebayes | |
| [2014-10-03 18:59] Calculating variation effects for Test1, freebayes | |
| [2014-10-03 18:59] snpEff effects : Test1 | |
| [2014-10-03 18:59] | |
| [2014-10-03 18:59] WARNINGS: Some warning were detected | |
| [2014-10-03 18:59] Warning type Number of warnings | |
| [2014-10-03 18:59] WARNING_TRANSCRIPT_INCOMPLETE 19 | |
| [2014-10-03 18:59] WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS 9 | |
| [2014-10-03 18:59] | |
| [2014-10-03 18:59] | |
| [2014-10-03 18:59] tabix index TestBatch1-effects.vcf.gz | |
| [2014-10-03 18:59] Filtering for Test1, freebayes | |
| [2014-10-03 18:59] bgzip TestBatch1-effects-ploidyfix.vcf | |
| [2014-10-03 18:59] tabix index TestBatch1-effects-ploidyfix.vcf.gz | |
| [2014-10-03 18:59] Hard filtering /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/TestBatch1-effects-ploidyfix.vcf.gz with (AF[0] <= 0.5 && (DP < 4 || (DP < 13 && %QUAL < 10))) || (AF[0] > 0.5 && (DP < 4 && %QUAL < 50)) || (%QUAL < 458.0 && DP > 229 && AF[0] <= 0.5) : Test1 | |
| [2014-10-03 18:59] tabix index TestBatch1-effects-ploidyfix-filter.vcf.gz | |
| [2014-10-03 18:59] multiprocessing: split_variants_by_sample | |
| [2014-10-03 18:59] Timing: prepped BAM merging | |
| [2014-10-03 18:59] multiprocessing: delayed_bam_merge | |
| [2014-10-03 18:59] Merge bam files to 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 18:59] Index BAM file: 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 18:59] Timing: validation | |
| [2014-10-03 18:59] multiprocessing: compare_to_rm | |
| [2014-10-03 18:59] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 18:59] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 18:59] Comparing variant calls using bcbio.variation : Test1 | |
| [2014-10-03 18:59] 2014-10-03 18:59:26,209 [INFO ] MLog clients using log4j logging. | |
| [2014-10-03 18:59] 2014-10-03 18:59:26,472 [INFO ] State :begin :: {:desc "Starting variation analysis"} | |
| [2014-10-03 18:59] 2014-10-03 18:59:26,503 [INFO ] State :clean :: {:desc "Cleaning input VCF: ref"} | |
| [2014-10-03 18:59] 2014-10-03 18:59:26,714 [INFO ] State :merge :: {:desc "Merging multiple input files: ref"} | |
| [2014-10-03 18:59] 2014-10-03 18:59:26,715 [INFO ] State :prep :: {:desc "Prepare VCF, resorting to genome build: ref"} | |
| [2014-10-03 18:59] INFO 18:59:29,855 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:29,856 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:29,858 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:29,858 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:29,861 HelpFormatter - Program Args: -T SelectVariants --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-ref-prep.vcf --unsafe ALL --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/txtmp5196216138041461096/Test1-ref-noref.vcf --excludeNonVariants --excludeFiltered -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 18:59] INFO 18:59:29,863 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:29,864 HelpFormatter - Date/Time: 2014/10/03 18:59:29 | |
| [2014-10-03 18:59] INFO 18:59:29,864 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:29,865 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:30,442 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:30,506 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:30,525 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 18:59] INFO 18:59:30,562 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:30,563 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:30,564 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:30,564 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:30,568 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 18:59] INFO 18:59:30,621 SelectVariants - 9 records processed. | |
| [2014-10-03 18:59] INFO 18:59:30,623 ProgressMeter - done 9.00e+00 0.0 s 109.0 m 1.0% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:30,624 ProgressMeter - Total runtime 0.06 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:30,717 NativeMethodAccessorImpl - State :normalize :: {:desc "Normalize MNP and indel variants: ref"} | |
| [2014-10-03 18:59] INFO 18:59:30,785 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:30,786 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:30,787 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:30,787 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:30,788 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/txtmp9174654483491916994/Test1-ref-noref-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-ref-noref.vcf | |
| [2014-10-03 18:59] INFO 18:59:30,788 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:30,789 HelpFormatter - Date/Time: 2014/10/03 18:59:30 | |
| [2014-10-03 18:59] INFO 18:59:30,789 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:30,790 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:30,794 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:30,817 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:30,823 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:30,824 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:30,824 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:30,825 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] 0 variants were aligned | |
| [2014-10-03 18:59] INFO 18:59:30,869 ProgressMeter - done 9.00e+00 0.0 s 82.8 m 0.4% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:30,872 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:31,043 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:31,049 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:31,050 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:31,051 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:31,051 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/txtmp4166789971769638741/Test1-ref-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-ref-worknomnp.vcf | |
| [2014-10-03 18:59] INFO 18:59:31,052 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:31,057 HelpFormatter - Date/Time: 2014/10/03 18:59:31 | |
| [2014-10-03 18:59] INFO 18:59:31,057 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:31,058 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:31,062 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:31,077 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:31,080 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:31,080 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:31,081 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:31,082 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] 0 variants were aligned | |
| [2014-10-03 18:59] INFO 18:59:31,099 ProgressMeter - done 9.00e+00 0.0 s 31.8 m 0.4% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:31,099 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:31,161 NativeMethodAccessorImpl - State :clean :: {:desc "Cleaning input VCF: eval"} | |
| [2014-10-03 18:59] INFO 18:59:31,161 NativeMethodAccessorImpl - State :merge :: {:desc "Merging multiple input files: eval"} | |
| [2014-10-03 18:59] INFO 18:59:31,162 NativeMethodAccessorImpl - State :prep :: {:desc "Prepare VCF, resorting to genome build: eval"} | |
| [2014-10-03 18:59] INFO 18:59:31,246 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:31,247 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:31,247 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:31,248 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:31,248 HelpFormatter - Program Args: -T SelectVariants --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/Test1-effects-ploidyfix-combined-gatkclean.vcf.gz --unsafe ALL --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/txtmp485873909619549333/Test1-eval-noref.vcf --excludeNonVariants --excludeFiltered -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 18:59] INFO 18:59:31,249 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:31,249 HelpFormatter - Date/Time: 2014/10/03 18:59:31 | |
| [2014-10-03 18:59] INFO 18:59:31,250 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:31,250 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:31,270 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:31,287 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:31,290 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 18:59] WARN 18:59:31,291 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 18:59] INFO 18:59:31,292 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:31,293 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:31,293 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:31,294 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:31,294 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 18:59] INFO 18:59:31,337 SelectVariants - 10 records processed. | |
| [2014-10-03 18:59] INFO 18:59:31,340 ProgressMeter - done 1.00e+01 0.0 s 76.9 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:31,340 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:31,403 NativeMethodAccessorImpl - State :normalize :: {:desc "Normalize MNP and indel variants: eval"} | |
| [2014-10-03 18:59] INFO 18:59:31,432 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:31,434 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:31,434 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:31,436 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:31,437 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/txtmp3792386914070100019/Test1-eval-noref-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-eval-noref.vcf | |
| [2014-10-03 18:59] INFO 18:59:31,438 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:31,438 HelpFormatter - Date/Time: 2014/10/03 18:59:31 | |
| [2014-10-03 18:59] INFO 18:59:31,438 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:31,439 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:31,444 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:31,457 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:31,460 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:31,460 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:31,461 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:31,461 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] 0 variants were aligned | |
| [2014-10-03 18:59] INFO 18:59:31,496 ProgressMeter - done 9.00e+00 0.0 s 65.0 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:31,497 ProgressMeter - Total runtime 0.04 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:31,659 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:31,664 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:31,665 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:31,666 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:31,666 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/txtmp1332528497007531748/Test1-eval-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-eval-worknomnp.vcf | |
| [2014-10-03 18:59] INFO 18:59:31,667 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:31,667 HelpFormatter - Date/Time: 2014/10/03 18:59:31 | |
| [2014-10-03 18:59] INFO 18:59:31,668 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:31,668 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:31,671 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:31,708 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:31,722 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:31,722 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:31,723 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:31,724 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] 0 variants were aligned | |
| [2014-10-03 18:59] INFO 18:59:31,758 ProgressMeter - done 9.00e+00 0.0 s 64.3 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:31,759 ProgressMeter - Total runtime 0.04 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:31,828 NativeMethodAccessorImpl - State :combine :: {:desc "Creating merged VCF files for all comparisons"} | |
| [2014-10-03 18:59] INFO 18:59:31,830 NativeMethodAccessorImpl - State :annotate :: {:desc "Annotate VCFs with metrics"} | |
| [2014-10-03 18:59] INFO 18:59:31,831 NativeMethodAccessorImpl - State :filter :: {:desc "Post annotation filtering"} | |
| [2014-10-03 18:59] INFO 18:59:31,841 NativeMethodAccessorImpl - State :compare :: {:desc "Comparing VCFs: ref vs eval"} | |
| [2014-10-03 18:59] INFO 18:59:32,027 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:32,028 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:32,029 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:32,031 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:32,032 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-eval-nomnp-nosv.vcf --concordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-ref-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/txtmp8173734152147687930/Test1-eval-ref-concordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 18:59] INFO 18:59:32,033 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:32,033 HelpFormatter - Date/Time: 2014/10/03 18:59:32 | |
| [2014-10-03 18:59] INFO 18:59:32,034 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:32,034 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:32,045 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:32,057 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:32,069 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 18:59] INFO 18:59:32,070 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:32,071 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:32,071 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:32,072 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:32,072 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 18:59] INFO 18:59:32,077 SelectVariants - Selecting only variants concordant with the track: concordance | |
| [2014-10-03 18:59] INFO 18:59:32,111 SelectVariants - 9 records processed. | |
| [2014-10-03 18:59] INFO 18:59:32,117 ProgressMeter - done 1.00e+01 0.0 s 76.2 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:32,118 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:32,233 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:32,234 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:32,234 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:32,235 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:32,235 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-ref-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-eval-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/txtmp5948299972859053019/Test1-ref-eval-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 18:59] INFO 18:59:32,236 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:32,236 HelpFormatter - Date/Time: 2014/10/03 18:59:32 | |
| [2014-10-03 18:59] INFO 18:59:32,237 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:32,238 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:32,248 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:32,260 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:32,267 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 18:59] INFO 18:59:32,268 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:32,269 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:32,269 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:32,270 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:32,270 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 18:59] INFO 18:59:32,271 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 18:59] INFO 18:59:32,287 SelectVariants - 9 records processed. | |
| [2014-10-03 18:59] INFO 18:59:32,290 ProgressMeter - done 1.00e+01 0.0 s 33.4 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:32,291 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:32,379 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:32,380 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:32,380 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:32,380 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:32,381 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-eval-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-ref-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/txtmp7397726959443809352/Test1-eval-ref-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 18:59] INFO 18:59:32,382 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:32,382 HelpFormatter - Date/Time: 2014/10/03 18:59:32 | |
| [2014-10-03 18:59] INFO 18:59:32,383 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:32,383 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:32,389 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:32,401 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:32,407 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 18:59] INFO 18:59:32,408 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:32,409 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:32,409 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:32,410 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:32,411 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 18:59] INFO 18:59:32,411 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 18:59] INFO 18:59:32,436 SelectVariants - 9 records processed. | |
| [2014-10-03 18:59] INFO 18:59:32,437 ProgressMeter - done 1.00e+01 0.0 s 45.9 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:32,438 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:32,575 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:32,585 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:32,586 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:32,587 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:32,587 HelpFormatter - Program Args: -T VariantAnnotator --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.bam --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/Test1-ref-eval-discordance-asref.vcf --allow_potentially_misencoded_quality_scores -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/txtmp8041083308795220217/Test1-ref-eval-discordance-asref-annotated.vcf -A DepthOfCoverage -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/Test1-ref-eval-discordance-asref.vcf | |
| [2014-10-03 18:59] INFO 18:59:32,588 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:32,588 HelpFormatter - Date/Time: 2014/10/03 18:59:32 | |
| [2014-10-03 18:59] INFO 18:59:32,589 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:32,589 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:32,599 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:32,637 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 | |
| [2014-10-03 18:59] INFO 18:59:32,638 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 18:59] INFO 18:59:32,641 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.00 | |
| [2014-10-03 18:59] INFO 18:59:32,648 IntervalUtils - Processing 1 bp from intervals | |
| [2014-10-03 18:59] INFO 18:59:32,649 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 18:59] INFO 18:59:32,665 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:32,669 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:32,669 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:32,974 VariantAnnotator - Processed 1 loci. | |
| [2014-10-03 18:59] | |
| [2014-10-03 18:59] INFO 18:59:32,985 ProgressMeter - done 1.00e+00 0.0 s 87.9 h 0.0% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:32,986 ProgressMeter - Total runtime 0.32 secs, 0.01 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:32,987 MicroScheduler - 12 reads were filtered out during the traversal out of approximately 1152 total reads (1.04%) | |
| [2014-10-03 18:59] INFO 18:59:32,988 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 18:59] INFO 18:59:32,988 MicroScheduler - -> 11 reads (0.95% of total) failing DuplicateReadFilter | |
| [2014-10-03 18:59] INFO 18:59:32,989 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter | |
| [2014-10-03 18:59] INFO 18:59:32,989 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 18:59] INFO 18:59:32,990 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 18:59] INFO 18:59:32,990 MicroScheduler - -> 1 reads (0.09% of total) failing UnmappedReadFilter | |
| [2014-10-03 18:59] INFO 18:59:33,122 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:33,123 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:33,123 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:33,124 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:33,124 HelpFormatter - Program Args: -T CombineVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/txtmp3799059055154670916/Test1-eval-ref-discordance-fullcombine.vcf --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null --variant:v0 /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/Test1-eval-ref-discordance.vcf --variant:v1 /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/Test1-ref-eval-discordance-asref-annotated.vcf --genotypemergeoption PRIORITIZE | |
| [2014-10-03 18:59] INFO 18:59:33,125 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:33,125 HelpFormatter - Date/Time: 2014/10/03 18:59:33 | |
| [2014-10-03 18:59] INFO 18:59:33,126 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:33,126 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:33,136 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:33,154 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:33,163 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:33,163 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:33,164 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:33,164 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:33,182 ProgressMeter - done 2.00e+00 0.0 s 2.5 h 84.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:33,189 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:33,312 NativeMethodAccessorImpl - State :summary :: {:desc "Summarize comparisons"} | |
| [2014-10-03 18:59] INFO 18:59:35,064 C3P0Registry - Initializing c3p0-0.9.1.2 [built 21-May-2007 15:04:56; debug? true; trace: 10] | |
| [2014-10-03 18:59] INFO 18:59:35,125 AbstractPoolBackedDataSource - Initializing c3p0 pool... com.mchange.v2.c3p0.ComboPooledDataSource [ acquireIncrement -> 3, acquireRetryAttempts -> 30, acquireRetryDelay -> 1000, autoCommitOnClose -> false, automaticTestTable -> null, breakAfterAcquireFailure -> false, checkoutTimeout -> 0, connectionCustomizerClassName -> null, connectionTesterClassName -> com.mchange.v2.c3p0.impl.DefaultConnectionTester, dataSourceName -> 2rvy8f941nrdvynkzcfs5|3e55d650, debugUnreturnedConnectionStackTraces -> false, description -> null, driverClass -> org.sqlite.JDBC, factoryClassLocation -> null, forceIgnoreUnresolvedTransactions -> false, identityToken -> 2rvy8f941nrdvynkzcfs5|3e55d650, idleConnectionTestPeriod -> 0, initialPoolSize -> 3, jdbcUrl -> jdbc:sqlite:/home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/Test1-eval-ref-discordance-annotate-gemini.db, maxAdministrativeTaskTime -> 0, maxConnectionAge -> 0, maxIdleTime -> 0, maxIdleTimeExcessConnections -> 0, maxPoolSize -> 15, maxStatements -> 0, maxStatementsPerConnection -> 0, minPoolSize -> 3, numHelperThreads -> 3, numThreadsAwaitingCheckoutDefaultUser -> 0, preferredTestQuery -> null, properties -> {}, propertyCycle -> 0, testConnectionOnCheckin -> false, testConnectionOnCheckout -> false, unreturnedConnectionTimeout -> 0, usesTraditionalReflectiveProxies -> false ] | |
| [2014-10-03 18:59] INFO 18:59:35,359 NativeMethodAccessorImpl - State :finished :: {:desc "Finished"} | |
| [2014-10-03 18:59] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 18:59] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 18:59] Comparing variant calls using bcbio.variation : Test1 | |
| [2014-10-03 18:59] 2014-10-03 18:59:38,340 [INFO ] MLog clients using log4j logging. | |
| [2014-10-03 18:59] 2014-10-03 18:59:38,603 [INFO ] State :begin :: {:desc "Starting variation analysis"} | |
| [2014-10-03 18:59] 2014-10-03 18:59:38,631 [INFO ] State :clean :: {:desc "Cleaning input VCF: ref"} | |
| [2014-10-03 18:59] 2014-10-03 18:59:38,863 [INFO ] State :merge :: {:desc "Merging multiple input files: ref"} | |
| [2014-10-03 18:59] 2014-10-03 18:59:38,864 [INFO ] State :prep :: {:desc "Prepare VCF, resorting to genome build: ref"} | |
| [2014-10-03 18:59] INFO 18:59:41,874 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:41,876 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:41,877 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:41,877 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:41,880 HelpFormatter - Program Args: -T SelectVariants --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-ref-prep.vcf --unsafe ALL --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/txtmp4712499941512396493/Test1-ref-noref.vcf --excludeNonVariants --excludeFiltered -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 18:59] INFO 18:59:41,884 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:41,885 HelpFormatter - Date/Time: 2014/10/03 18:59:41 | |
| [2014-10-03 18:59] INFO 18:59:41,885 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:41,886 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:42,489 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:42,556 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:42,573 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 18:59] INFO 18:59:42,625 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:42,627 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:42,628 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:42,629 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:42,634 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 18:59] INFO 18:59:42,699 SelectVariants - 9 records processed. | |
| [2014-10-03 18:59] INFO 18:59:42,702 ProgressMeter - done 9.00e+00 0.0 s 2.3 h 1.0% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:42,704 ProgressMeter - Total runtime 0.08 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:42,798 NativeMethodAccessorImpl - State :normalize :: {:desc "Normalize MNP and indel variants: ref"} | |
| [2014-10-03 18:59] INFO 18:59:42,860 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:42,860 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:42,861 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:42,861 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:42,862 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/txtmp6198459933708596847/Test1-ref-noref-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-ref-noref.vcf | |
| [2014-10-03 18:59] INFO 18:59:42,862 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:42,863 HelpFormatter - Date/Time: 2014/10/03 18:59:42 | |
| [2014-10-03 18:59] INFO 18:59:42,864 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:42,864 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:42,869 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:42,894 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:42,897 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:42,898 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:42,898 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:42,899 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] 0 variants were aligned | |
| [2014-10-03 18:59] INFO 18:59:42,942 ProgressMeter - done 9.00e+00 0.0 s 80.0 m 0.4% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:42,943 ProgressMeter - Total runtime 0.04 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:43,117 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:43,120 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:43,121 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:43,122 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:43,122 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/txtmp5213284978751793615/Test1-ref-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-ref-worknomnp.vcf | |
| [2014-10-03 18:59] INFO 18:59:43,123 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:43,123 HelpFormatter - Date/Time: 2014/10/03 18:59:43 | |
| [2014-10-03 18:59] INFO 18:59:43,124 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:43,124 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:43,134 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:43,160 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:43,163 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:43,164 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:43,164 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:43,164 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] 0 variants were aligned | |
| [2014-10-03 18:59] INFO 18:59:43,182 ProgressMeter - done 9.00e+00 0.0 s 31.8 m 0.4% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:43,182 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:43,249 NativeMethodAccessorImpl - State :clean :: {:desc "Cleaning input VCF: eval"} | |
| [2014-10-03 18:59] INFO 18:59:43,250 NativeMethodAccessorImpl - State :merge :: {:desc "Merging multiple input files: eval"} | |
| [2014-10-03 18:59] INFO 18:59:43,251 NativeMethodAccessorImpl - State :prep :: {:desc "Prepare VCF, resorting to genome build: eval"} | |
| [2014-10-03 18:59] INFO 18:59:43,337 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:43,338 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:43,338 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:43,339 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:43,339 HelpFormatter - Program Args: -T SelectVariants --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/Test1-effects-ploidyfix-filter.vcf.gz --unsafe ALL --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/txtmp6911998313145380693/Test1-eval-noref.vcf --excludeNonVariants --excludeFiltered -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 18:59] INFO 18:59:43,340 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:43,341 HelpFormatter - Date/Time: 2014/10/03 18:59:43 | |
| [2014-10-03 18:59] INFO 18:59:43,341 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:43,342 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:43,363 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:43,379 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:43,383 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 18:59] WARN 18:59:43,384 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 18:59] INFO 18:59:43,385 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:43,386 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:43,386 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:43,387 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:43,388 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 18:59] INFO 18:59:43,460 SelectVariants - 11 records processed. | |
| [2014-10-03 18:59] INFO 18:59:43,462 ProgressMeter - done 1.10e+01 0.0 s 114.4 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:43,463 ProgressMeter - Total runtime 0.08 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:43,534 NativeMethodAccessorImpl - State :normalize :: {:desc "Normalize MNP and indel variants: eval"} | |
| [2014-10-03 18:59] INFO 18:59:43,579 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:43,584 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:43,585 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:43,586 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:43,586 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/txtmp8810209022048376983/Test1-eval-noref-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-eval-noref.vcf | |
| [2014-10-03 18:59] INFO 18:59:43,587 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:43,587 HelpFormatter - Date/Time: 2014/10/03 18:59:43 | |
| [2014-10-03 18:59] INFO 18:59:43,592 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:43,593 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:43,596 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:43,610 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:43,613 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:43,614 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:43,614 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:43,615 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] 0 variants were aligned | |
| [2014-10-03 18:59] INFO 18:59:43,640 ProgressMeter - done 1.10e+01 0.0 s 38.0 m 84.4% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:43,641 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:43,782 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:43,783 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:43,784 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:43,784 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:43,784 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/txtmp1612984902111138008/Test1-eval-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-eval-worknomnp.vcf | |
| [2014-10-03 18:59] INFO 18:59:43,785 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:43,786 HelpFormatter - Date/Time: 2014/10/03 18:59:43 | |
| [2014-10-03 18:59] INFO 18:59:43,786 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:43,786 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:43,800 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:43,832 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:43,843 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:43,844 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:43,844 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:43,845 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] 0 variants were aligned | |
| [2014-10-03 18:59] INFO 18:59:43,877 ProgressMeter - done 1.10e+01 0.0 s 49.6 m 84.4% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:43,878 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:43,950 NativeMethodAccessorImpl - State :combine :: {:desc "Creating merged VCF files for all comparisons"} | |
| [2014-10-03 18:59] INFO 18:59:43,952 NativeMethodAccessorImpl - State :annotate :: {:desc "Annotate VCFs with metrics"} | |
| [2014-10-03 18:59] INFO 18:59:43,953 NativeMethodAccessorImpl - State :filter :: {:desc "Post annotation filtering"} | |
| [2014-10-03 18:59] INFO 18:59:43,981 NativeMethodAccessorImpl - State :compare :: {:desc "Comparing VCFs: ref vs eval"} | |
| [2014-10-03 18:59] INFO 18:59:44,196 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:44,197 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:44,198 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:44,198 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:44,199 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-eval-nomnp-nosv.vcf --concordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-ref-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/txtmp6298802197063143896/Test1-eval-ref-concordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 18:59] INFO 18:59:44,199 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:44,205 HelpFormatter - Date/Time: 2014/10/03 18:59:44 | |
| [2014-10-03 18:59] INFO 18:59:44,206 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:44,206 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:44,221 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:44,233 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:44,245 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 18:59] INFO 18:59:44,246 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:44,247 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:44,247 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:44,248 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:44,248 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 18:59] INFO 18:59:44,253 SelectVariants - Selecting only variants concordant with the track: concordance | |
| [2014-10-03 18:59] INFO 18:59:44,288 SelectVariants - 11 records processed. | |
| [2014-10-03 18:59] INFO 18:59:44,290 ProgressMeter - done 1.10e+01 0.0 s 64.1 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:44,291 ProgressMeter - Total runtime 0.04 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:44,406 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:44,407 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:44,412 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:44,413 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:44,413 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-ref-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-eval-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/txtmp8144041383318594441/Test1-ref-eval-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 18:59] INFO 18:59:44,414 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:44,414 HelpFormatter - Date/Time: 2014/10/03 18:59:44 | |
| [2014-10-03 18:59] INFO 18:59:44,415 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:44,415 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:44,422 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:44,434 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:44,441 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 18:59] INFO 18:59:44,441 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:44,442 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:44,442 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:44,443 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:44,444 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 18:59] INFO 18:59:44,448 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 18:59] INFO 18:59:44,460 SelectVariants - 9 records processed. | |
| [2014-10-03 18:59] INFO 18:59:44,462 ProgressMeter - done 1.10e+01 0.0 s 29.0 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:44,463 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:44,548 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:44,549 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:44,550 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:44,550 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:44,550 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-eval-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-ref-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/txtmp4230848199946294402/Test1-eval-ref-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 18:59] INFO 18:59:44,551 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:44,552 HelpFormatter - Date/Time: 2014/10/03 18:59:44 | |
| [2014-10-03 18:59] INFO 18:59:44,552 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:44,553 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:44,562 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:44,588 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:44,597 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 18:59] INFO 18:59:44,598 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:44,598 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:44,599 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:44,600 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:44,602 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 18:59] INFO 18:59:44,606 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 18:59] INFO 18:59:44,625 SelectVariants - 11 records processed. | |
| [2014-10-03 18:59] INFO 18:59:44,627 ProgressMeter - done 1.10e+01 0.0 s 42.1 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:44,628 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:44,750 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:44,756 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:44,760 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:44,761 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:44,761 HelpFormatter - Program Args: -T VariantAnnotator --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.bam --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/Test1-ref-eval-discordance-asref.vcf --allow_potentially_misencoded_quality_scores -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/txtmp1693297223452580339/Test1-ref-eval-discordance-asref-annotated.vcf -A DepthOfCoverage -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/Test1-ref-eval-discordance-asref.vcf | |
| [2014-10-03 18:59] INFO 18:59:44,762 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:44,763 HelpFormatter - Date/Time: 2014/10/03 18:59:44 | |
| [2014-10-03 18:59] INFO 18:59:44,764 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:44,764 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:44,776 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:44,792 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 | |
| [2014-10-03 18:59] INFO 18:59:44,793 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 18:59] INFO 18:59:44,795 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.00 | |
| [2014-10-03 18:59] WARN 18:59:44,799 IntervalUtils - The interval file /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/Test1-ref-eval-discordance-asref.vcf contains no intervals that could be parsed. | |
| [2014-10-03 18:59] INFO 18:59:44,800 IntervalUtils - Processing 0 bp from intervals | |
| [2014-10-03 18:59] WARN 18:59:44,802 GenomeAnalysisEngine - The given combination of -L and -XL options results in an empty set. No intervals to process. | |
| [2014-10-03 18:59] INFO 18:59:44,803 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 18:59] INFO 18:59:44,805 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:44,806 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:44,806 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:44,823 VariantAnnotator - Processed 0 loci. | |
| [2014-10-03 18:59] | |
| [2014-10-03 18:59] INFO 18:59:44,826 ProgressMeter - done 0.00e+00 0.0 s 5.2 h 0.0% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:44,827 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:44,917 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:44,918 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:44,919 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:44,919 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:44,920 HelpFormatter - Program Args: -T CombineVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/txtmp4941983863869545287/Test1-eval-ref-discordance-fullcombine.vcf --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null --variant:v0 /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/Test1-eval-ref-discordance.vcf --variant:v1 /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/Test1-ref-eval-discordance-asref-annotated.vcf --genotypemergeoption PRIORITIZE | |
| [2014-10-03 18:59] INFO 18:59:44,920 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:44,921 HelpFormatter - Date/Time: 2014/10/03 18:59:44 | |
| [2014-10-03 18:59] INFO 18:59:44,921 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:44,922 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:44,928 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:44,941 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:44,948 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:44,949 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:44,949 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:44,950 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:44,961 ProgressMeter - done 2.00e+00 0.0 s 97.9 m 84.4% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:44,963 ProgressMeter - Total runtime 0.01 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:45,046 NativeMethodAccessorImpl - State :summary :: {:desc "Summarize comparisons"} | |
| [2014-10-03 18:59] INFO 18:59:47,266 C3P0Registry - Initializing c3p0-0.9.1.2 [built 21-May-2007 15:04:56; debug? true; trace: 10] | |
| [2014-10-03 18:59] INFO 18:59:47,358 AbstractPoolBackedDataSource - Initializing c3p0 pool... com.mchange.v2.c3p0.ComboPooledDataSource [ acquireIncrement -> 3, acquireRetryAttempts -> 30, acquireRetryDelay -> 1000, autoCommitOnClose -> false, automaticTestTable -> null, breakAfterAcquireFailure -> false, checkoutTimeout -> 0, connectionCustomizerClassName -> null, connectionTesterClassName -> com.mchange.v2.c3p0.impl.DefaultConnectionTester, dataSourceName -> 2rvy8f941nre5dqzrbh3l|6fe32564, debugUnreturnedConnectionStackTraces -> false, description -> null, driverClass -> org.sqlite.JDBC, factoryClassLocation -> null, forceIgnoreUnresolvedTransactions -> false, identityToken -> 2rvy8f941nre5dqzrbh3l|6fe32564, idleConnectionTestPeriod -> 0, initialPoolSize -> 3, jdbcUrl -> jdbc:sqlite:/home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/Test1-eval-ref-discordance-annotate-gemini.db, maxAdministrativeTaskTime -> 0, maxConnectionAge -> 0, maxIdleTime -> 0, maxIdleTimeExcessConnections -> 0, maxPoolSize -> 15, maxStatements -> 0, maxStatementsPerConnection -> 0, minPoolSize -> 3, numHelperThreads -> 3, numThreadsAwaitingCheckoutDefaultUser -> 0, preferredTestQuery -> null, properties -> {}, propertyCycle -> 0, testConnectionOnCheckin -> false, testConnectionOnCheckout -> false, unreturnedConnectionTimeout -> 0, usesTraditionalReflectiveProxies -> false ] | |
| [2014-10-03 18:59] INFO 18:59:47,621 NativeMethodAccessorImpl - State :finished :: {:desc "Finished"} | |
| [2014-10-03 18:59] Timing: ensemble calling | |
| [2014-10-03 18:59] multiprocessing: combine_calls | |
| [2014-10-03 18:59] Ensemble consensus calls for TestBatch1: gatk,freebayes | |
| [2014-10-03 18:59] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 18:59] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 18:59] Ensemble calling: TestBatch1 | |
| [2014-10-03 18:59] 2014-10-03 18:59:50,526 [INFO ] MLog clients using log4j logging. | |
| [2014-10-03 18:59] 2014-10-03 18:59:51,083 [INFO ] State :begin :: {:desc "Starting variation analysis"} | |
| [2014-10-03 18:59] 2014-10-03 18:59:51,149 [INFO ] State :clean :: {:desc "Cleaning input VCF: combo"} | |
| [2014-10-03 18:59] 2014-10-03 18:59:51,151 [INFO ] State :merge :: {:desc "Merging multiple input files: combo"} | |
| [2014-10-03 18:59] 2014-10-03 18:59:51,151 [INFO ] State :prep :: {:desc "Prepare VCF, resorting to genome build: combo"} | |
| [2014-10-03 18:59] 2014-10-03 18:59:51,173 [INFO ] State :normalize :: {:desc "Normalize MNP and indel variants: combo"} | |
| [2014-10-03 18:59] INFO 18:59:53,889 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:53,894 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:53,895 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:53,895 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:53,898 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/txtmp8892481243817266490/Test1-effects-ploidyfix-combined-gatkclean-leftalign.vcf.gz --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/Test1-effects-ploidyfix-combined-gatkclean.vcf.gz | |
| [2014-10-03 18:59] INFO 18:59:53,902 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:53,903 HelpFormatter - Date/Time: 2014/10/03 18:59:53 | |
| [2014-10-03 18:59] INFO 18:59:53,904 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:53,904 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:54,530 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:54,608 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] WARN 18:59:54,620 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 18:59] INFO 18:59:54,669 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:54,670 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:54,670 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:54,671 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] 0 variants were aligned | |
| [2014-10-03 18:59] INFO 18:59:54,775 ProgressMeter - done 1.00e+01 0.0 s 2.9 h 84.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:54,777 ProgressMeter - Total runtime 0.11 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:54,989 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:54,991 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:54,992 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:54,992 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:54,993 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/txtmp6160330195930887881/Test1-combo-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-worknomnp.vcf | |
| [2014-10-03 18:59] INFO 18:59:54,994 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:54,994 HelpFormatter - Date/Time: 2014/10/03 18:59:54 | |
| [2014-10-03 18:59] INFO 18:59:54,995 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:54,996 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:55,004 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:55,027 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:55,044 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:55,046 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:55,047 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:55,048 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] 0 variants were aligned | |
| [2014-10-03 18:59] INFO 18:59:55,107 ProgressMeter - done 1.00e+01 0.0 s 99.1 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:55,108 ProgressMeter - Total runtime 0.06 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:55,199 NativeMethodAccessorImpl - State :clean :: {:desc "Cleaning input VCF: gatk"} | |
| [2014-10-03 18:59] INFO 18:59:55,205 NativeMethodAccessorImpl - State :merge :: {:desc "Merging multiple input files: gatk"} | |
| [2014-10-03 18:59] INFO 18:59:55,206 NativeMethodAccessorImpl - State :prep :: {:desc "Prepare VCF, resorting to genome build: gatk"} | |
| [2014-10-03 18:59] INFO 18:59:55,211 NativeMethodAccessorImpl - State :normalize :: {:desc "Normalize MNP and indel variants: gatk"} | |
| [2014-10-03 18:59] INFO 18:59:55,301 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:55,302 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:55,302 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:55,303 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:55,303 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/txtmp5738619142322070246/Test1-effects-ploidyfix-combined-gatkclean-leftalign.vcf.gz --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/Test1-effects-ploidyfix-combined-gatkclean.vcf.gz | |
| [2014-10-03 18:59] INFO 18:59:55,304 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:55,304 HelpFormatter - Date/Time: 2014/10/03 18:59:55 | |
| [2014-10-03 18:59] INFO 18:59:55,305 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:55,305 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:55,317 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:55,349 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] WARN 18:59:55,354 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 18:59] INFO 18:59:55,361 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:55,361 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:55,362 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:55,363 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] 0 variants were aligned | |
| [2014-10-03 18:59] INFO 18:59:55,383 ProgressMeter - done 1.00e+01 0.0 s 34.7 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:55,384 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:55,521 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:55,521 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:55,523 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:55,523 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:55,524 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/txtmp944359586503439850/Test1-gatk-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-worknomnp.vcf | |
| [2014-10-03 18:59] INFO 18:59:55,524 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:55,525 HelpFormatter - Date/Time: 2014/10/03 18:59:55 | |
| [2014-10-03 18:59] INFO 18:59:55,525 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:55,526 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:55,529 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:55,541 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:55,547 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:55,547 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:55,548 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:55,548 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] 0 variants were aligned | |
| [2014-10-03 18:59] INFO 18:59:55,569 ProgressMeter - done 1.00e+01 0.0 s 34.1 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:55,569 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:55,635 NativeMethodAccessorImpl - State :clean :: {:desc "Cleaning input VCF: freebayes"} | |
| [2014-10-03 18:59] INFO 18:59:55,636 NativeMethodAccessorImpl - State :merge :: {:desc "Merging multiple input files: freebayes"} | |
| [2014-10-03 18:59] INFO 18:59:55,637 NativeMethodAccessorImpl - State :prep :: {:desc "Prepare VCF, resorting to genome build: freebayes"} | |
| [2014-10-03 18:59] INFO 18:59:55,641 NativeMethodAccessorImpl - State :normalize :: {:desc "Normalize MNP and indel variants: freebayes"} | |
| [2014-10-03 18:59] INFO 18:59:55,694 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:55,695 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:55,696 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:55,698 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:55,699 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/txtmp3526488451609187884/Test1-effects-ploidyfix-filter-leftalign.vcf.gz --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/Test1-effects-ploidyfix-filter.vcf.gz | |
| [2014-10-03 18:59] INFO 18:59:55,700 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:55,700 HelpFormatter - Date/Time: 2014/10/03 18:59:55 | |
| [2014-10-03 18:59] INFO 18:59:55,701 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:55,701 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:55,705 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:55,734 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] WARN 18:59:55,738 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 18:59] INFO 18:59:55,742 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:55,743 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:55,743 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:55,744 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] 0 variants were aligned | |
| [2014-10-03 18:59] INFO 18:59:55,786 ProgressMeter - done 1.20e+01 0.0 s 59.1 m 84.4% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:55,788 ProgressMeter - Total runtime 0.04 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:55,989 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:55,992 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:55,993 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:55,994 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:55,994 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/txtmp1390023150438383299/Test1-freebayes-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-freebayes-worknomnp.vcf | |
| [2014-10-03 18:59] INFO 18:59:55,995 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:55,995 HelpFormatter - Date/Time: 2014/10/03 18:59:55 | |
| [2014-10-03 18:59] INFO 18:59:55,996 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:55,996 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:56,003 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:56,046 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:56,058 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:56,059 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:56,059 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:56,060 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] 0 variants were aligned | |
| [2014-10-03 18:59] INFO 18:59:56,110 ProgressMeter - done 1.20e+01 0.0 s 70.1 m 84.4% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:56,117 ProgressMeter - Total runtime 0.06 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:56,202 NativeMethodAccessorImpl - State :combine :: {:desc "Creating merged VCF files for all comparisons"} | |
| [2014-10-03 18:59] INFO 18:59:56,204 NativeMethodAccessorImpl - State :annotate :: {:desc "Annotate VCFs with metrics"} | |
| [2014-10-03 18:59] INFO 18:59:56,206 NativeMethodAccessorImpl - State :filter :: {:desc "Post annotation filtering"} | |
| [2014-10-03 18:59] INFO 18:59:56,300 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:56,300 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:56,301 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:56,302 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:56,302 HelpFormatter - Program Args: -T CombineVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/txtmp3836041860598742249/Test1-combo-nomnp-mincombine.vcf --rod_priority_list combo,gatk,freebayes --variant:combo /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp.vcf --variant:gatk /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-nomnp.vcf --variant:freebayes /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-freebayes-nomnp.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION --sites_only --minimalVCF | |
| [2014-10-03 18:59] INFO 18:59:56,303 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:56,303 HelpFormatter - Date/Time: 2014/10/03 18:59:56 | |
| [2014-10-03 18:59] INFO 18:59:56,304 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:56,304 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:56,316 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:56,336 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:56,379 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 18:59] INFO 18:59:56,385 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:56,385 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:56,386 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:56,388 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:56,393 CombineVariants - Pre-stripping genotypes for performance | |
| [2014-10-03 18:59] INFO 18:59:56,470 ProgressMeter - done 1.10e+01 0.0 s 2.1 h 98.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:56,471 ProgressMeter - Total runtime 0.08 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:56,720 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:56,722 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:56,723 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:56,723 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:56,724 HelpFormatter - Program Args: -T SelectVariants --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp-mincombine-fix-consensus.vcf --unsafe ALL --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/txtmp5284387438419850476/Test1-combo-nomnp-mincombine-fix-consensus-cleaned.vcf --excludeNonVariants --excludeFiltered | |
| [2014-10-03 18:59] INFO 18:59:56,725 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:56,725 HelpFormatter - Date/Time: 2014/10/03 18:59:56 | |
| [2014-10-03 18:59] INFO 18:59:56,726 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:56,726 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:56,738 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:56,751 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:56,754 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:56,755 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:56,756 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:56,757 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:56,758 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 18:59] INFO 18:59:56,802 SelectVariants - 11 records processed. | |
| [2014-10-03 18:59] INFO 18:59:56,804 ProgressMeter - done 1.10e+01 0.0 s 72.9 m 84.4% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:56,806 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:56,890 GeneratedMethodAccessor34 - State :compare :: {:desc "Comparing VCFs: combo vs gatk"} | |
| [2014-10-03 18:59] INFO 18:59:57,024 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:57,031 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:57,032 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:57,032 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:57,033 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-nomnp-nosv.vcf --concordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp-mincombine-fix-consensus-cleaned-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp5389481466782016817/Test1-gatk-combo-concordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 18:59] INFO 18:59:57,035 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:57,035 HelpFormatter - Date/Time: 2014/10/03 18:59:57 | |
| [2014-10-03 18:59] INFO 18:59:57,036 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:57,037 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:57,046 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:57,068 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:57,096 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 18:59] INFO 18:59:57,097 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:57,098 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:57,098 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:57,099 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:57,104 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 18:59] INFO 18:59:57,108 SelectVariants - Selecting only variants concordant with the track: concordance | |
| [2014-10-03 18:59] INFO 18:59:57,134 SelectVariants - 10 records processed. | |
| [2014-10-03 18:59] INFO 18:59:57,136 ProgressMeter - done 1.10e+01 0.0 s 56.8 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:57,137 ProgressMeter - Total runtime 0.04 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:57,230 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:57,231 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:57,232 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:57,232 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:57,233 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp-mincombine-fix-consensus-cleaned-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp7428464665487393568/Test1-combo-gatk-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 18:59] INFO 18:59:57,233 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:57,234 HelpFormatter - Date/Time: 2014/10/03 18:59:57 | |
| [2014-10-03 18:59] INFO 18:59:57,234 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:57,235 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:57,241 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:57,253 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:57,260 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 18:59] INFO 18:59:57,261 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:57,262 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:57,263 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:57,263 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:57,264 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 18:59] INFO 18:59:57,272 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 18:59] INFO 18:59:57,296 SelectVariants - 11 records processed. | |
| [2014-10-03 18:59] INFO 18:59:57,299 ProgressMeter - done 1.10e+01 0.0 s 54.7 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:57,300 ProgressMeter - Total runtime 0.04 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:57,417 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:57,420 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:57,421 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:57,422 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:57,422 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp-mincombine-fix-consensus-cleaned-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp7634465010176188968/Test1-gatk-combo-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 18:59] INFO 18:59:57,423 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:57,424 HelpFormatter - Date/Time: 2014/10/03 18:59:57 | |
| [2014-10-03 18:59] INFO 18:59:57,424 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:57,424 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:57,445 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:57,470 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:57,483 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 18:59] INFO 18:59:57,484 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:57,485 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:57,485 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:57,486 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:57,488 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 18:59] INFO 18:59:57,490 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 18:59] INFO 18:59:57,509 SelectVariants - 10 records processed. | |
| [2014-10-03 18:59] INFO 18:59:57,510 ProgressMeter - done 1.10e+01 0.0 s 37.8 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:57,511 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:57,581 GeneratedMethodAccessor34 - State :compare :: {:desc "Comparing VCFs: combo vs freebayes"} | |
| [2014-10-03 18:59] INFO 18:59:57,690 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:57,691 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:57,691 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:57,692 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:57,692 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-freebayes-nomnp-nosv.vcf --concordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp-mincombine-fix-consensus-cleaned-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp3683387343591931914/Test1-freebayes-combo-concordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 18:59] INFO 18:59:57,693 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:57,693 HelpFormatter - Date/Time: 2014/10/03 18:59:57 | |
| [2014-10-03 18:59] INFO 18:59:57,694 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:57,694 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:57,700 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:57,713 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:57,726 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 18:59] INFO 18:59:57,727 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:57,728 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:57,729 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:57,730 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:57,730 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 18:59] INFO 18:59:57,732 SelectVariants - Selecting only variants concordant with the track: concordance | |
| [2014-10-03 18:59] INFO 18:59:57,757 SelectVariants - 11 records processed. | |
| [2014-10-03 18:59] INFO 18:59:57,763 ProgressMeter - done 1.10e+01 0.0 s 50.7 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:57,764 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:57,898 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:57,899 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:57,900 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:57,901 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:57,901 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp-mincombine-fix-consensus-cleaned-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-freebayes-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp6577183358584048185/Test1-combo-freebayes-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 18:59] INFO 18:59:57,904 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:57,904 HelpFormatter - Date/Time: 2014/10/03 18:59:57 | |
| [2014-10-03 18:59] INFO 18:59:57,905 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:57,905 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:57,917 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:57,943 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:57,954 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 18:59] INFO 18:59:57,960 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:57,962 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:57,962 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:57,963 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:57,963 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 18:59] INFO 18:59:57,965 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 18:59] INFO 18:59:57,981 SelectVariants - 11 records processed. | |
| [2014-10-03 18:59] INFO 18:59:57,983 ProgressMeter - done 1.10e+01 0.0 s 31.0 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:57,984 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:58,073 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:58,074 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:58,075 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:58,075 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:58,076 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-freebayes-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp-mincombine-fix-consensus-cleaned-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp7969981643647262832/Test1-freebayes-combo-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 18:59] INFO 18:59:58,076 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:58,077 HelpFormatter - Date/Time: 2014/10/03 18:59:58 | |
| [2014-10-03 18:59] INFO 18:59:58,078 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:58,078 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:58,092 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:58,128 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:58,144 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 18:59] INFO 18:59:58,146 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:58,146 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:58,147 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:58,148 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:58,148 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 18:59] INFO 18:59:58,150 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 18:59] INFO 18:59:58,165 SelectVariants - 11 records processed. | |
| [2014-10-03 18:59] INFO 18:59:58,167 ProgressMeter - done 1.10e+01 0.0 s 29.6 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:58,167 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:58,234 GeneratedMethodAccessor34 - State :compare :: {:desc "Comparing VCFs: gatk vs freebayes"} | |
| [2014-10-03 18:59] INFO 18:59:58,324 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:58,327 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:58,328 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:58,328 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:58,328 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-freebayes-nomnp-nosv.vcf --concordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp6956473533762127003/Test1-freebayes-gatk-concordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 18:59] INFO 18:59:58,329 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:58,333 HelpFormatter - Date/Time: 2014/10/03 18:59:58 | |
| [2014-10-03 18:59] INFO 18:59:58,334 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:58,335 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:58,339 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:58,356 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:58,367 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 18:59] INFO 18:59:58,369 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:58,370 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:58,370 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:58,371 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:58,371 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 18:59] INFO 18:59:58,375 SelectVariants - Selecting only variants concordant with the track: concordance | |
| [2014-10-03 18:59] INFO 18:59:58,392 SelectVariants - 11 records processed. | |
| [2014-10-03 18:59] INFO 18:59:58,394 ProgressMeter - done 1.10e+01 0.0 s 34.8 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:58,394 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:58,486 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:58,486 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:58,487 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:58,488 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:58,488 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-freebayes-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp6083026182000508354/Test1-gatk-freebayes-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 18:59] INFO 18:59:58,489 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:58,489 HelpFormatter - Date/Time: 2014/10/03 18:59:58 | |
| [2014-10-03 18:59] INFO 18:59:58,490 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:58,490 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:58,499 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:58,520 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:58,537 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 18:59] INFO 18:59:58,538 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:58,540 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:58,541 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:58,542 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:58,544 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 18:59] INFO 18:59:58,546 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 18:59] INFO 18:59:58,574 SelectVariants - 10 records processed. | |
| [2014-10-03 18:59] INFO 18:59:58,576 ProgressMeter - done 1.10e+01 0.0 s 52.7 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:58,577 ProgressMeter - Total runtime 0.04 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:58,661 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:58,662 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:58,663 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:58,663 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:58,664 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-freebayes-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp7799271068124219378/Test1-freebayes-gatk-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 18:59] INFO 18:59:58,664 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:58,665 HelpFormatter - Date/Time: 2014/10/03 18:59:58 | |
| [2014-10-03 18:59] INFO 18:59:58,665 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:58,666 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:58,676 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:58,695 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:58,702 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 18:59] INFO 18:59:58,704 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:58,705 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:58,705 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:58,706 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:58,706 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 18:59] INFO 18:59:58,707 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 18:59] INFO 18:59:58,720 SelectVariants - 11 records processed. | |
| [2014-10-03 18:59] INFO 18:59:58,722 ProgressMeter - done 1.10e+01 0.0 s 24.9 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:58,722 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:58,803 GeneratedMethodAccessor34 - State :finalize :: {:desc "Finalize multiple: combo"} | |
| [2014-10-03 18:59] INFO 18:59:58,831 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:58,832 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:58,832 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:58,834 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:58,834 HelpFormatter - Program Args: -T CombineVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/multiple/txtmp8585413023874044882/Test1-multiall-fullcombine.vcf --rod_priority_list comboANDgatk,comboANDfreebayes,gatkANDfreebayes --variant:comboANDgatk /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/Test1-gatk-combo-concordance.vcf --variant:comboANDfreebayes /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/Test1-freebayes-combo-concordance.vcf --variant:gatkANDfreebayes /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/Test1-freebayes-gatk-concordance.vcf --genotypemergeoption PRIORITIZE | |
| [2014-10-03 18:59] INFO 18:59:58,835 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:58,835 HelpFormatter - Date/Time: 2014/10/03 18:59:58 | |
| [2014-10-03 18:59] INFO 18:59:58,836 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:58,836 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:58,848 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:58,862 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:58,871 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:58,872 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:58,872 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:58,872 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:58,898 ProgressMeter - done 1.10e+01 0.0 s 39.6 m 84.4% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:58,899 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:58,988 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:58,988 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:58,989 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:58,990 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:58,990 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/multiple/txtmp3778425097747331195/Test1-multiall-fullcombine-Intersection.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/multiple/Test1-multiall-fullcombine.vcf -select set == 'Intersection' | |
| [2014-10-03 18:59] INFO 18:59:58,991 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:58,991 HelpFormatter - Date/Time: 2014/10/03 18:59:58 | |
| [2014-10-03 18:59] INFO 18:59:58,992 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:58,992 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:58,997 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:59,008 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:59,011 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:59,011 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:59,011 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:59,011 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:59,060 SelectVariants - 11 records processed. | |
| [2014-10-03 18:59] INFO 18:59:59,061 ProgressMeter - done 1.10e+01 0.0 s 75.7 m 84.4% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:59,063 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:59,155 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:59,156 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:59,156 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:59,157 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:59,157 HelpFormatter - Program Args: -T CombineVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/multiple/txtmp3490372733748341434/Test1-multinocombo-fullcombine.vcf --rod_priority_list gatkANDfreebayes --variant:gatkANDfreebayes /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/Test1-freebayes-gatk-concordance.vcf --genotypemergeoption PRIORITIZE | |
| [2014-10-03 18:59] INFO 18:59:59,158 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:59,158 HelpFormatter - Date/Time: 2014/10/03 18:59:59 | |
| [2014-10-03 18:59] INFO 18:59:59,159 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:59,159 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:59,165 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:59,177 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:59,180 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:59,183 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:59,184 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:59,185 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:59,214 ProgressMeter - done 1.00e+01 0.0 s 50.6 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:59,217 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:59,317 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:59,318 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:59,319 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:59,319 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:59,320 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/multiple/txtmp4089484652698695725/Test1-multinocombo-fullcombine-Intersection.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/multiple/Test1-multinocombo-fullcombine.vcf -select set == 'Intersection' | |
| [2014-10-03 18:59] INFO 18:59:59,321 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:59,321 HelpFormatter - Date/Time: 2014/10/03 18:59:59 | |
| [2014-10-03 18:59] INFO 18:59:59,322 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:59,322 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:59,329 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:59,350 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:59,360 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:59,361 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:59,361 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:59,362 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:59,395 SelectVariants - 10 records processed. | |
| [2014-10-03 18:59] INFO 18:59:59,401 ProgressMeter - done 1.00e+01 0.0 s 66.1 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:59,402 ProgressMeter - Total runtime 0.04 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:59,573 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:59,574 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 18:59] INFO 18:59:59,575 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 18:59] INFO 18:59:59,576 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 18:59] INFO 18:59:59,581 HelpFormatter - Program Args: -T CombineVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/multiple/txtmp5906963055898997983/Test1-multiall-nocombo-fullcombine.vcf --rod_priority_list truep,combo --variant:truep /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/multiple/Test1-multiall-fullcombine-Intersection.vcf --variant:combo /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/multiple/Test1-multinocombo-fullcombine-Intersection.vcf --genotypemergeoption PRIORITIZE | |
| [2014-10-03 18:59] INFO 18:59:59,581 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 18:59] INFO 18:59:59,583 HelpFormatter - Date/Time: 2014/10/03 18:59:59 | |
| [2014-10-03 18:59] INFO 18:59:59,583 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:59,584 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 18:59] INFO 18:59:59,591 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 18:59] INFO 18:59:59,628 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 18:59] INFO 18:59:59,645 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:59,646 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 18:59] INFO 18:59:59,647 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 18:59] INFO 18:59:59,647 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 18:59] INFO 18:59:59,689 ProgressMeter - done 1.00e+01 0.0 s 70.6 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 18:59] INFO 18:59:59,690 ProgressMeter - Total runtime 0.04 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 18:59] INFO 18:59:59,878 GeneratedMethodAccessor34 - State :finalize :: {:desc "Finalize recal-filter: combo, gatk"} | |
| [2014-10-03 19:00] INFO 19:00:01,637 C3P0Registry - Initializing c3p0-0.9.1.2 [built 21-May-2007 15:04:56; debug? true; trace: 10] | |
| [2014-10-03 19:00] Filter VCF with {{:variant-type :complex, :attr-key :all, :zygosity :het} nil, {:variant-type :complex, :attr-key :all, :zygosity :hom} #<SMO SMO | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] Kernel used: | |
| [2014-10-03 19:00] Linear Kernel: K(x,y) = <x,y> | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] Classifier for classes: pass, fail | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] BinarySMO | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] Machine linear: showing attribute weights, not support vectors. | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] + 1 | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] Number of kernel evaluations: 0 | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] >, {:variant-type :snp, :attr-key :all, :zygosity :het} nil, {:variant-type :snp, :attr-key :all, :zygosity :hom} nil} | |
| [2014-10-03 19:00] Filter VCF with {{:variant-type :complex, :attr-key :calling, :zygosity :het} nil, {:variant-type :complex, :attr-key :calling, :zygosity :hom} #<SMO SMO | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] Kernel used: | |
| [2014-10-03 19:00] Linear Kernel: K(x,y) = <x,y> | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] Classifier for classes: pass, fail | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] BinarySMO | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] Machine linear: showing attribute weights, not support vectors. | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] + 1 | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] Number of kernel evaluations: 0 | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] >, {:variant-type :snp, :attr-key :calling, :zygosity :het} nil, {:variant-type :snp, :attr-key :calling, :zygosity :hom} #<SMO SMO | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] Kernel used: | |
| [2014-10-03 19:00] Linear Kernel: K(x,y) = <x,y> | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] Classifier for classes: pass, fail | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] BinarySMO | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] Machine linear: showing attribute weights, not support vectors. | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] - 1 | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] Number of kernel evaluations: 0 | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] >, {:variant-type :complex, :attr-key :balance, :zygosity :het} nil, {:variant-type :complex, :attr-key :balance, :zygosity :hom} #<SMO SMO | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] Kernel used: | |
| [2014-10-03 19:00] Linear Kernel: K(x,y) = <x,y> | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] Classifier for classes: pass, fail | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] BinarySMO | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] Machine linear: showing attribute weights, not support vectors. | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] + 1 | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] Number of kernel evaluations: 0 | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] >, {:variant-type :snp, :attr-key :balance, :zygosity :het} nil, {:variant-type :snp, :attr-key :balance, :zygosity :hom} #<SMO SMO | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] Kernel used: | |
| [2014-10-03 19:00] Linear Kernel: K(x,y) = <x,y> | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] Classifier for classes: pass, fail | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] BinarySMO | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] Machine linear: showing attribute weights, not support vectors. | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] - 1 | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] Number of kernel evaluations: 0 | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] >} | |
| [2014-10-03 19:00] INFO 19:00:06,538 GeneratedMethodAccessor34 - State :compare :: {:desc "Comparing VCFs: combo-recal vs gatk"} | |
| [2014-10-03 19:00] INFO 19:00:06,573 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:06,574 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:00] INFO 19:00:06,575 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:00] INFO 19:00:06,575 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:00] INFO 19:00:06,576 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-nomnp-nosv.vcf --concordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp-mincombine-fix-consensus-cleaned-nosv-nofilter-cfilter.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp5765560860377096740/Test1-gatk-combo-recal-concordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:00] INFO 19:00:06,577 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:00] INFO 19:00:06,577 HelpFormatter - Date/Time: 2014/10/03 19:00:06 | |
| [2014-10-03 19:00] INFO 19:00:06,578 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:06,578 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:06,589 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:00] INFO 19:00:06,629 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:00] INFO 19:00:06,647 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:00] INFO 19:00:06,647 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:06,648 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:06,648 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:00] INFO 19:00:06,649 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:00] INFO 19:00:06,649 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:00] INFO 19:00:06,652 SelectVariants - Selecting only variants concordant with the track: concordance | |
| [2014-10-03 19:00] INFO 19:00:06,687 SelectVariants - 10 records processed. | |
| [2014-10-03 19:00] INFO 19:00:06,697 ProgressMeter - done 1.10e+01 0.0 s 73.5 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:00] INFO 19:00:06,698 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:00] INFO 19:00:06,807 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:06,816 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:00] INFO 19:00:06,817 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:00] INFO 19:00:06,818 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:00] INFO 19:00:06,818 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp-mincombine-fix-consensus-cleaned-nosv-nofilter-cfilter.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp901633079881184343/Test1-combo-recal-gatk-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:00] INFO 19:00:06,819 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:00] INFO 19:00:06,819 HelpFormatter - Date/Time: 2014/10/03 19:00:06 | |
| [2014-10-03 19:00] INFO 19:00:06,820 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:06,820 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:06,833 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:00] INFO 19:00:06,859 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:00] INFO 19:00:06,864 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:00] INFO 19:00:06,865 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:06,866 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:06,866 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:00] INFO 19:00:06,867 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:00] INFO 19:00:06,868 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:00] INFO 19:00:06,870 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:00] INFO 19:00:06,878 SelectVariants - 11 records processed. | |
| [2014-10-03 19:00] INFO 19:00:06,880 ProgressMeter - done 1.10e+01 0.0 s 20.0 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:00] INFO 19:00:06,880 ProgressMeter - Total runtime 0.01 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:00] INFO 19:00:06,982 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:06,988 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:00] INFO 19:00:06,989 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:00] INFO 19:00:06,989 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:00] INFO 19:00:06,990 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp-mincombine-fix-consensus-cleaned-nosv-nofilter-cfilter.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp3319852092111134424/Test1-gatk-combo-recal-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:00] INFO 19:00:06,991 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:00] INFO 19:00:06,991 HelpFormatter - Date/Time: 2014/10/03 19:00:06 | |
| [2014-10-03 19:00] INFO 19:00:06,992 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:06,992 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:07,000 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:00] INFO 19:00:07,014 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:00] INFO 19:00:07,018 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:00] INFO 19:00:07,019 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:07,019 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:07,020 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:00] INFO 19:00:07,020 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:00] INFO 19:00:07,021 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:00] INFO 19:00:07,022 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:00] INFO 19:00:07,040 SelectVariants - 10 records processed. | |
| [2014-10-03 19:00] INFO 19:00:07,042 ProgressMeter - done 1.10e+01 0.0 s 33.6 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:00] INFO 19:00:07,043 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:00] INFO 19:00:07,124 GeneratedMethodAccessor34 - State :summary :: {:desc "Summarize comparisons"} | |
| [2014-10-03 19:00] INFO 19:00:07,321 GeneratedMethodAccessor34 - State :finished :: {:desc "Finished"} | |
| [2014-10-03 19:00] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:00] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:00] Comparing variant calls using bcbio.variation : Test1 | |
| [2014-10-03 19:00] 2014-10-03 19:00:10,346 [INFO ] MLog clients using log4j logging. | |
| [2014-10-03 19:00] 2014-10-03 19:00:10,610 [INFO ] State :begin :: {:desc "Starting variation analysis"} | |
| [2014-10-03 19:00] 2014-10-03 19:00:10,639 [INFO ] State :clean :: {:desc "Cleaning input VCF: ref"} | |
| [2014-10-03 19:00] 2014-10-03 19:00:10,863 [INFO ] State :merge :: {:desc "Merging multiple input files: ref"} | |
| [2014-10-03 19:00] 2014-10-03 19:00:10,864 [INFO ] State :prep :: {:desc "Prepare VCF, resorting to genome build: ref"} | |
| [2014-10-03 19:00] INFO 19:00:13,813 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:13,815 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:00] INFO 19:00:13,816 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:00] INFO 19:00:13,816 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:00] INFO 19:00:13,819 HelpFormatter - Program Args: -T SelectVariants --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-ref-prep.vcf --unsafe ALL --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/txtmp4679673503966679978/Test1-ref-noref.vcf --excludeNonVariants --excludeFiltered -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:00] INFO 19:00:13,822 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:00] INFO 19:00:13,822 HelpFormatter - Date/Time: 2014/10/03 19:00:13 | |
| [2014-10-03 19:00] INFO 19:00:13,823 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:13,823 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:14,409 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:00] INFO 19:00:14,470 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:00] INFO 19:00:14,486 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:00] INFO 19:00:14,534 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:14,535 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:14,535 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:00] INFO 19:00:14,536 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:00] INFO 19:00:14,540 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:00] INFO 19:00:14,609 SelectVariants - 9 records processed. | |
| [2014-10-03 19:00] INFO 19:00:14,612 ProgressMeter - done 9.00e+00 0.0 s 2.3 h 1.0% 0.0 s 0.0 s | |
| [2014-10-03 19:00] INFO 19:00:14,613 ProgressMeter - Total runtime 0.08 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:00] INFO 19:00:14,707 NativeMethodAccessorImpl - State :normalize :: {:desc "Normalize MNP and indel variants: ref"} | |
| [2014-10-03 19:00] INFO 19:00:14,760 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:14,763 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:00] INFO 19:00:14,764 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:00] INFO 19:00:14,765 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:00] INFO 19:00:14,765 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/txtmp7861009552762679358/Test1-ref-noref-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-ref-noref.vcf | |
| [2014-10-03 19:00] INFO 19:00:14,766 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:00] INFO 19:00:14,766 HelpFormatter - Date/Time: 2014/10/03 19:00:14 | |
| [2014-10-03 19:00] INFO 19:00:14,767 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:14,767 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:14,772 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:00] INFO 19:00:14,794 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:00] INFO 19:00:14,805 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:14,806 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:14,806 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:00] INFO 19:00:14,807 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:00] 0 variants were aligned | |
| [2014-10-03 19:00] INFO 19:00:14,847 ProgressMeter - done 9.00e+00 0.0 s 74.4 m 0.4% 0.0 s 0.0 s | |
| [2014-10-03 19:00] INFO 19:00:14,848 ProgressMeter - Total runtime 0.04 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:00] INFO 19:00:15,017 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:15,018 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:00] INFO 19:00:15,018 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:00] INFO 19:00:15,018 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:00] INFO 19:00:15,018 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/txtmp3707169732376032586/Test1-ref-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-ref-worknomnp.vcf | |
| [2014-10-03 19:00] INFO 19:00:15,018 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:00] INFO 19:00:15,018 HelpFormatter - Date/Time: 2014/10/03 19:00:15 | |
| [2014-10-03 19:00] INFO 19:00:15,018 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:15,018 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:15,030 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:00] INFO 19:00:15,050 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:00] INFO 19:00:15,053 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:15,054 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:15,054 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:00] INFO 19:00:15,054 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:00] 0 variants were aligned | |
| [2014-10-03 19:00] INFO 19:00:15,073 ProgressMeter - done 9.00e+00 0.0 s 35.6 m 0.4% 0.0 s 0.0 s | |
| [2014-10-03 19:00] INFO 19:00:15,074 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:00] INFO 19:00:15,137 NativeMethodAccessorImpl - State :clean :: {:desc "Cleaning input VCF: eval"} | |
| [2014-10-03 19:00] INFO 19:00:15,138 NativeMethodAccessorImpl - State :merge :: {:desc "Merging multiple input files: eval"} | |
| [2014-10-03 19:00] INFO 19:00:15,139 NativeMethodAccessorImpl - State :prep :: {:desc "Prepare VCF, resorting to genome build: eval"} | |
| [2014-10-03 19:00] INFO 19:00:15,222 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:15,223 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:00] INFO 19:00:15,224 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:00] INFO 19:00:15,224 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:00] INFO 19:00:15,225 HelpFormatter - Program Args: -T SelectVariants --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble.vcf --unsafe ALL --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/txtmp3563955467002397842/Test1-eval-noref.vcf --excludeNonVariants --excludeFiltered -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:00] INFO 19:00:15,225 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:00] INFO 19:00:15,226 HelpFormatter - Date/Time: 2014/10/03 19:00:15 | |
| [2014-10-03 19:00] INFO 19:00:15,226 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:15,227 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:15,242 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:00] INFO 19:00:15,258 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:00] INFO 19:00:15,263 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:00] INFO 19:00:15,264 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:15,265 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:15,266 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:00] INFO 19:00:15,266 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:00] INFO 19:00:15,267 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:00] INFO 19:00:15,328 SelectVariants - 11 records processed. | |
| [2014-10-03 19:00] INFO 19:00:15,329 ProgressMeter - done 1.10e+01 0.0 s 96.0 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:00] INFO 19:00:15,330 ProgressMeter - Total runtime 0.06 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:00] INFO 19:00:15,405 NativeMethodAccessorImpl - State :normalize :: {:desc "Normalize MNP and indel variants: eval"} | |
| [2014-10-03 19:00] INFO 19:00:15,451 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:15,458 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:00] INFO 19:00:15,459 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:00] INFO 19:00:15,459 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:00] INFO 19:00:15,460 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/txtmp8185644299791067736/Test1-eval-noref-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-eval-noref.vcf | |
| [2014-10-03 19:00] INFO 19:00:15,460 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:00] INFO 19:00:15,461 HelpFormatter - Date/Time: 2014/10/03 19:00:15 | |
| [2014-10-03 19:00] INFO 19:00:15,461 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:15,462 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:15,467 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:00] INFO 19:00:15,481 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:00] INFO 19:00:15,486 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:15,487 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:15,487 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:00] INFO 19:00:15,488 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:00] 0 variants were aligned | |
| [2014-10-03 19:00] INFO 19:00:15,518 ProgressMeter - done 1.00e+01 0.0 s 50.0 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 19:00] INFO 19:00:15,519 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:00] INFO 19:00:15,663 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:15,666 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:00] INFO 19:00:15,667 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:00] INFO 19:00:15,673 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:00] INFO 19:00:15,674 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/txtmp5273791431920463109/Test1-eval-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-eval-worknomnp.vcf | |
| [2014-10-03 19:00] INFO 19:00:15,675 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:00] INFO 19:00:15,675 HelpFormatter - Date/Time: 2014/10/03 19:00:15 | |
| [2014-10-03 19:00] INFO 19:00:15,676 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:15,676 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:15,682 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:00] INFO 19:00:15,719 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:00] INFO 19:00:15,728 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:15,728 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:15,729 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:00] INFO 19:00:15,730 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:00] 0 variants were aligned | |
| [2014-10-03 19:00] INFO 19:00:15,749 ProgressMeter - done 1.00e+01 0.0 s 33.6 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 19:00] INFO 19:00:15,750 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:00] INFO 19:00:15,823 NativeMethodAccessorImpl - State :combine :: {:desc "Creating merged VCF files for all comparisons"} | |
| [2014-10-03 19:00] INFO 19:00:15,825 NativeMethodAccessorImpl - State :annotate :: {:desc "Annotate VCFs with metrics"} | |
| [2014-10-03 19:00] INFO 19:00:15,826 NativeMethodAccessorImpl - State :filter :: {:desc "Post annotation filtering"} | |
| [2014-10-03 19:00] INFO 19:00:15,836 NativeMethodAccessorImpl - State :compare :: {:desc "Comparing VCFs: ref vs eval"} | |
| [2014-10-03 19:00] INFO 19:00:16,075 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:16,080 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:00] INFO 19:00:16,081 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:00] INFO 19:00:16,082 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:00] INFO 19:00:16,082 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-eval-nomnp-nosv.vcf --concordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-ref-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/txtmp891267368842390225/Test1-eval-ref-concordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:00] INFO 19:00:16,083 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:00] INFO 19:00:16,084 HelpFormatter - Date/Time: 2014/10/03 19:00:16 | |
| [2014-10-03 19:00] INFO 19:00:16,084 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:16,085 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:16,094 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:00] INFO 19:00:16,106 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:00] INFO 19:00:16,120 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:00] INFO 19:00:16,121 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:16,122 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:16,123 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:00] INFO 19:00:16,123 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:00] INFO 19:00:16,124 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:00] INFO 19:00:16,126 SelectVariants - Selecting only variants concordant with the track: concordance | |
| [2014-10-03 19:00] INFO 19:00:16,169 SelectVariants - 10 records processed. | |
| [2014-10-03 19:00] INFO 19:00:16,171 ProgressMeter - done 1.00e+01 0.0 s 79.8 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:00] INFO 19:00:16,172 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:00] INFO 19:00:16,290 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:16,290 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:00] INFO 19:00:16,291 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:00] INFO 19:00:16,291 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:00] INFO 19:00:16,292 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-ref-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-eval-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/txtmp3130498288466855860/Test1-ref-eval-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:00] INFO 19:00:16,293 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:00] INFO 19:00:16,293 HelpFormatter - Date/Time: 2014/10/03 19:00:16 | |
| [2014-10-03 19:00] INFO 19:00:16,294 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:16,294 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:16,301 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:00] INFO 19:00:16,314 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:00] INFO 19:00:16,321 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:00] INFO 19:00:16,322 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:16,323 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:16,323 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:00] INFO 19:00:16,324 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:00] INFO 19:00:16,325 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:00] INFO 19:00:16,328 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:00] INFO 19:00:16,342 SelectVariants - 9 records processed. | |
| [2014-10-03 19:00] INFO 19:00:16,344 ProgressMeter - done 1.00e+01 0.0 s 33.2 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:00] INFO 19:00:16,344 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:00] INFO 19:00:16,432 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:16,433 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:00] INFO 19:00:16,434 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:00] INFO 19:00:16,434 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:00] INFO 19:00:16,435 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-eval-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-ref-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/txtmp6999399197408594975/Test1-eval-ref-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:00] INFO 19:00:16,435 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:00] INFO 19:00:16,436 HelpFormatter - Date/Time: 2014/10/03 19:00:16 | |
| [2014-10-03 19:00] INFO 19:00:16,436 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:16,437 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:16,442 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:00] INFO 19:00:16,454 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:00] INFO 19:00:16,461 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:00] INFO 19:00:16,462 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:16,463 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:16,463 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:00] INFO 19:00:16,464 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:00] INFO 19:00:16,464 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:00] INFO 19:00:16,469 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:00] INFO 19:00:16,485 SelectVariants - 10 records processed. | |
| [2014-10-03 19:00] INFO 19:00:16,486 ProgressMeter - done 1.00e+01 0.0 s 38.3 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:00] INFO 19:00:16,487 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:00] INFO 19:00:16,586 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:16,587 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:00] INFO 19:00:16,587 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:00] INFO 19:00:16,588 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:00] INFO 19:00:16,588 HelpFormatter - Program Args: -T VariantAnnotator --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.bam --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/Test1-ref-eval-discordance-asref.vcf --allow_potentially_misencoded_quality_scores -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/txtmp2680097090357636942/Test1-ref-eval-discordance-asref-annotated.vcf -A DepthOfCoverage -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/Test1-ref-eval-discordance-asref.vcf | |
| [2014-10-03 19:00] INFO 19:00:16,589 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:00] INFO 19:00:16,589 HelpFormatter - Date/Time: 2014/10/03 19:00:16 | |
| [2014-10-03 19:00] INFO 19:00:16,590 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:16,590 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:16,601 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:00] INFO 19:00:16,620 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 | |
| [2014-10-03 19:00] INFO 19:00:16,621 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 19:00] INFO 19:00:16,623 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.00 | |
| [2014-10-03 19:00] WARN 19:00:16,636 IntervalUtils - The interval file /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/Test1-ref-eval-discordance-asref.vcf contains no intervals that could be parsed. | |
| [2014-10-03 19:00] INFO 19:00:16,637 IntervalUtils - Processing 0 bp from intervals | |
| [2014-10-03 19:00] WARN 19:00:16,637 GenomeAnalysisEngine - The given combination of -L and -XL options results in an empty set. No intervals to process. | |
| [2014-10-03 19:00] INFO 19:00:16,638 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 19:00] INFO 19:00:16,640 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:16,644 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:00] INFO 19:00:16,645 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:00] INFO 19:00:16,677 VariantAnnotator - Processed 0 loci. | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] INFO 19:00:16,679 ProgressMeter - done 0.00e+00 0.0 s 9.5 h 0.0% 0.0 s 0.0 s | |
| [2014-10-03 19:00] INFO 19:00:16,680 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:00] INFO 19:00:16,788 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:16,789 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:00] INFO 19:00:16,790 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:00] INFO 19:00:16,797 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:00] INFO 19:00:16,798 HelpFormatter - Program Args: -T CombineVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/txtmp2287889466247823441/Test1-eval-ref-discordance-fullcombine.vcf --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null --variant:v0 /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/Test1-eval-ref-discordance.vcf --variant:v1 /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/Test1-ref-eval-discordance-asref-annotated.vcf --genotypemergeoption PRIORITIZE | |
| [2014-10-03 19:00] INFO 19:00:16,798 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:00] INFO 19:00:16,799 HelpFormatter - Date/Time: 2014/10/03 19:00:16 | |
| [2014-10-03 19:00] INFO 19:00:16,800 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:16,800 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] INFO 19:00:16,807 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:00] INFO 19:00:16,821 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:00] INFO 19:00:16,828 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:16,830 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:00] INFO 19:00:16,831 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:00] INFO 19:00:16,831 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:00] INFO 19:00:16,853 ProgressMeter - done 1.00e+00 0.0 s 6.1 h 84.7% 0.0 s 0.0 s | |
| [2014-10-03 19:00] INFO 19:00:16,854 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:00] INFO 19:00:16,936 NativeMethodAccessorImpl - State :summary :: {:desc "Summarize comparisons"} | |
| [2014-10-03 19:00] INFO 19:00:18,111 C3P0Registry - Initializing c3p0-0.9.1.2 [built 21-May-2007 15:04:56; debug? true; trace: 10] | |
| [2014-10-03 19:00] INFO 19:00:18,201 AbstractPoolBackedDataSource - Initializing c3p0 pool... com.mchange.v2.c3p0.ComboPooledDataSource [ acquireIncrement -> 3, acquireRetryAttempts -> 30, acquireRetryDelay -> 1000, autoCommitOnClose -> false, automaticTestTable -> null, breakAfterAcquireFailure -> false, checkoutTimeout -> 0, connectionCustomizerClassName -> null, connectionTesterClassName -> com.mchange.v2.c3p0.impl.DefaultConnectionTester, dataSourceName -> 2rvy8f941nret6j1wpxk3w|8e17cdd, debugUnreturnedConnectionStackTraces -> false, description -> null, driverClass -> org.sqlite.JDBC, factoryClassLocation -> null, forceIgnoreUnresolvedTransactions -> false, identityToken -> 2rvy8f941nret6j1wpxk3w|8e17cdd, idleConnectionTestPeriod -> 0, initialPoolSize -> 3, jdbcUrl -> jdbc:sqlite:/home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/Test1-eval-ref-discordance-annotate-gemini.db, maxAdministrativeTaskTime -> 0, maxConnectionAge -> 0, maxIdleTime -> 0, maxIdleTimeExcessConnections -> 0, maxPoolSize -> 15, maxStatements -> 0, maxStatementsPerConnection -> 0, minPoolSize -> 3, numHelperThreads -> 3, numThreadsAwaitingCheckoutDefaultUser -> 0, preferredTestQuery -> null, properties -> {}, propertyCycle -> 0, testConnectionOnCheckin -> false, testConnectionOnCheckout -> false, unreturnedConnectionTimeout -> 0, usesTraditionalReflectiveProxies -> false ] | |
| [2014-10-03 19:00] INFO 19:00:18,426 NativeMethodAccessorImpl - State :finished :: {:desc "Finished"} | |
| [2014-10-03 19:00] Timing: validation summary | |
| /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/pandas/core/frame.py:1706: UserWarning: Boolean Series key will be reindexed to match DataFrame index. | |
| "DataFrame index.", UserWarning) | |
| [2014-10-03 19:00] Timing: structural variation | |
| [2014-10-03 19:00] Timing: population database | |
| [2014-10-03 19:00] multiprocessing: prep_gemini_db | |
| [2014-10-03 19:00] Timing: quality control | |
| [2014-10-03 19:00] multiprocessing: pipeline_summary | |
| [2014-10-03 19:00] Generating summary files: ['', 'Test1'] | |
| [2014-10-03 19:00] FastQC: Test1 | |
| [2014-10-03 19:00] Started analysis of 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] Approx 5% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] Approx 10% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] Approx 15% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] Approx 20% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] Approx 25% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] Approx 30% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] Approx 35% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] Approx 40% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] Approx 45% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] Approx 50% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] Approx 55% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] Approx 60% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] Approx 65% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] Approx 70% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] Approx 75% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] Approx 80% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] Approx 85% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] Approx 90% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] Approx 95% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] Analysis complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:00] bamtools stats : Test1 | |
| [2014-10-03 19:00] There is no qsignature for this species: hg19 | |
| [2014-10-03 19:00] multiprocessing: qsignature_summary | |
| [2014-10-03 19:00] Timing: archive | |
| [2014-10-03 19:00] Timing: finished | |
| [2014-10-03 19:00] Storing directory in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/qc | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-ready.bam | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-ready.bam.bai | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-disc.bam | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-disc.bam.bai | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-sr.bam | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-sr.bam.bai | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-ensemble.vcf | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-gatk.vcf.gz | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-gatk.vcf.gz.tbi | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-freebayes.vcf.gz | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-freebayes.vcf.gz.tbi | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-validate.pdf | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/100326_FC6107FAAXX/programs.txt | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/100326_FC6107FAAXX/bcbio-nextgen.log | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/100326_FC6107FAAXX/bcbio-nextgen-commands.log | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/100326_FC6107FAAXX/project-summary.yaml | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/100326_FC6107FAAXX/TestBatch1-ensemble.vcf | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/100326_FC6107FAAXX/TestBatch1-gatk.vcf.gz | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/100326_FC6107FAAXX/TestBatch1-gatk.vcf.gz.tbi | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/100326_FC6107FAAXX/TestBatch1-freebayes.vcf.gz | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/100326_FC6107FAAXX/TestBatch1-freebayes.vcf.gz.tbi | |
| [2014-10-03 19:00] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/100326_FC6107FAAXX/grading-summary.csv | |
| ok | |
| Allow BAM files as input to pipeline. ... [2014-10-03 19:00] Using input YAML configuration: /home/vagrant/bcbio-nextgen/tests/data/automated/run_info-bam.yaml | |
| [2014-10-03 19:00] Checking sample YAML configuration: /home/vagrant/bcbio-nextgen/tests/data/automated/run_info-bam.yaml | |
| [2014-10-03 19:00] Testing minimum versions of installed programs | |
| [2014-10-03 19:00] Resource requests: bwa, sambamba, samtools; memory: 2.0; cores: 16, 1, 16 | |
| [2014-10-03 19:00] Configuring 1 jobs to run, using 1 cores each with 2.2g of memory reserved for each job | |
| [2014-10-03 19:00] Timing: alignment preparation | |
| [2014-10-03 19:00] multiprocessing: prep_align_inputs | |
| [2014-10-03 19:00] BAM to bgzipped fastq | |
| [2014-10-03 19:00] top - 19:00:33 up 2:21, 2 users, load average: 1.31, 0.64, 0.32 | |
| [2014-10-03 19:00] Tasks: 86 total, 1 running, 85 sleeping, 0 stopped, 0 zombie | |
| [2014-10-03 19:00] %Cpu(s): 5.0 us, 0.8 sy, 2.0 ni, 91.3 id, 0.9 wa, 0.0 hi, 0.1 si, 0.0 st | |
| [2014-10-03 19:00] KiB Mem: 1017856 total, 458768 used, 559088 free, 16648 buffers | |
| [2014-10-03 19:00] KiB Swap: 0 total, 0 used, 0 free. 193964 cached Mem | |
| [2014-10-03 19:00] | |
| [2014-10-03 19:00] PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND | |
| [2014-10-03 19:00] 1 root 20 0 33648 2384 952 S 0.0 0.2 0:00.45 init | |
| [2014-10-03 19:00] 2 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kthreadd | |
| [2014-10-03 19:00] 3 root 20 0 0 0 0 S 0.0 0.0 0:00.20 ksoftirqd/0 | |
| [2014-10-03 19:00] 4 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kworker/0:0 | |
| [2014-10-03 19:00] 5 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kworker/0:0H | |
| [2014-10-03 19:00] 7 root 20 0 0 0 0 S 0.0 0.0 0:01.15 rcu_sched | |
| [2014-10-03 19:00] 8 root 20 0 0 0 0 S 0.0 0.0 0:02.09 rcuos/0 | |
| [2014-10-03 19:00] 9 root 20 0 0 0 0 S 0.0 0.0 0:00.00 rcu_bh | |
| [2014-10-03 19:00] 10 root 20 0 0 0 0 S 0.0 0.0 0:00.00 rcuob/0 | |
| [2014-10-03 19:00] 11 root rt 0 0 0 0 S 0.0 0.0 0:00.00 migration/0 | |
| [2014-10-03 19:00] 12 root rt 0 0 0 0 S 0.0 0.0 0:00.14 watchdog/0 | |
| [2014-10-03 19:00] 13 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 khelper | |
| [2014-10-03 19:00] 14 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kdevtmpfs | |
| [2014-10-03 19:00] 15 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 netns | |
| [2014-10-03 19:00] 16 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 writeback | |
| [2014-10-03 19:00] 17 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kintegrityd | |
| [2014-10-03 19:00] 18 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 bioset | |
| [2014-10-03 19:00] 19 root 0 -20 0 0 0 S 0.0 0.0 0:00.03 kworker/u3:0 | |
| [2014-10-03 19:00] 20 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kblockd | |
| [2014-10-03 19:00] 21 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 ata_sff | |
| [2014-10-03 19:00] 22 root 20 0 0 0 0 S 0.0 0.0 0:00.00 khubd | |
| [2014-10-03 19:00] 23 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 md | |
| [2014-10-03 19:00] 24 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 devfreq_wq | |
| [2014-10-03 19:00] 25 root 20 0 0 0 0 S 0.0 0.0 0:01.62 kworker/0:1 | |
| [2014-10-03 19:00] 26 root 20 0 0 0 0 S 0.0 0.0 0:00.00 khungtaskd | |
| [2014-10-03 19:00] 27 root 20 0 0 0 0 S 0.0 0.0 0:00.38 kswapd0 | |
| [2014-10-03 19:00] 28 root 25 5 0 0 0 S 0.0 0.0 0:00.00 ksmd | |
| [2014-10-03 19:00] 29 root 39 19 0 0 0 S 0.0 0.0 0:00.09 khugepaged | |
| [2014-10-03 19:00] 30 root 20 0 0 0 0 S 0.0 0.0 0:00.00 fsnotify_ma+ | |
| [2014-10-03 19:00] 31 root 20 0 0 0 0 S 0.0 0.0 0:00.00 ecryptfs-kt+ | |
| [2014-10-03 19:00] 32 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 crypto | |
| [2014-10-03 19:00] 44 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kthrotld | |
| [2014-10-03 19:00] 64 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 deferwq | |
| [2014-10-03 19:00] 65 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 charger_man+ | |
| [2014-10-03 19:00] 106 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kpsmoused | |
| [2014-10-03 19:00] 107 root 20 0 0 0 0 S 0.0 0.0 0:00.00 scsi_eh_0 | |
| [2014-10-03 19:00] 108 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kworker/u2:2 | |
| [2014-10-03 19:00] 109 root 20 0 0 0 0 S 0.0 0.0 0:00.93 kworker/u2:3 | |
| [2014-10-03 19:00] 154 root 20 0 0 0 0 S 0.0 0.0 0:00.22 jbd2/sda1-8 | |
| [2014-10-03 19:00] 155 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 ext4-rsv-co+ | |
| [2014-10-03 19:00] 394 root 20 0 19604 756 432 S 0.0 0.1 0:00.04 upstart-ude+ | |
| [2014-10-03 19:00] 399 root 20 0 50100 1616 680 S 0.0 0.2 0:00.05 systemd-ude+ | |
| [2014-10-03 19:00] 431 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 iprt | |
| [2014-10-03 19:00] 434 root 0 -20 0 0 0 S 0.0 0.0 0:00.05 kworker/u3:1 | |
| [2014-10-03 19:00] 521 root 20 0 23420 956 640 S 0.0 0.1 0:00.02 rpcbind | |
| [2014-10-03 19:00] 526 root 20 0 15260 300 88 S 0.0 0.0 0:00.02 upstart-soc+ | |
| [2014-10-03 19:00] 564 root 20 0 10224 2292 0 S 0.0 0.2 0:00.00 dhclient | |
| [2014-10-03 19:00] 567 statd 20 0 21544 1144 684 S 0.0 0.1 0:00.00 rpc.statd | |
| [2014-10-03 19:00] 732 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 rpciod | |
| [2014-10-03 19:00] 776 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 nfsiod | |
| [2014-10-03 19:00] 826 root 20 0 15276 524 288 S 0.0 0.1 0:00.00 upstart-fil+ | |
| [2014-10-03 19:00] 855 root 20 0 25544 308 84 S 0.0 0.0 0:00.00 rpc.idmapd | |
| [2014-10-03 19:00] 866 syslog 20 0 257912 2816 324 S 0.0 0.3 0:00.02 rsyslogd | |
| [2014-10-03 19:00] 880 message+ 20 0 39184 956 584 S 0.0 0.1 0:00.19 dbus-daemon | |
| [2014-10-03 19:00] 897 root 20 0 43452 1336 988 S 0.0 0.1 0:00.00 systemd-log+ | |
| [2014-10-03 19:00] 931 root 20 0 14540 868 704 S 0.0 0.1 0:00.00 getty | |
| [2014-10-03 19:00] 934 root 20 0 14540 856 704 S 0.0 0.1 0:00.00 getty | |
| [2014-10-03 19:00] 939 root 20 0 14540 864 704 S 0.0 0.1 0:00.00 getty | |
| [2014-10-03 19:00] 940 root 20 0 14540 864 704 S 0.0 0.1 0:00.00 getty | |
| [2014-10-03 19:00] 942 root 20 0 14540 864 704 S 0.0 0.1 0:00.00 getty | |
| [2014-10-03 19:00] 965 root 20 0 61364 1608 932 S 0.0 0.2 0:00.00 sshd | |
| [2014-10-03 19:00] 969 root 20 0 4368 556 412 S 0.0 0.1 0:00.00 acpid | |
| [2014-10-03 19:00] 997 root 20 0 23656 824 612 S 0.0 0.1 0:00.01 cron | |
| [2014-10-03 19:00] 998 daemon 20 0 19140 164 0 S 0.0 0.0 0:00.00 atd | |
| [2014-10-03 19:00] 1015 root 20 0 216612 912 588 S 0.0 0.1 0:02.12 VBoxService | |
| [2014-10-03 19:00] 1041 root 20 0 182524 32608 820 S 0.0 3.2 0:00.12 puppet | |
| [2014-10-03 19:00] 1071 root 20 0 112692 33824 384 S 0.0 3.3 0:00.00 ruby | |
| [2014-10-03 19:00] 1098 root 20 0 14540 860 700 S 0.0 0.1 0:00.00 getty | |
| [2014-10-03 19:00] 1168 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kauditd | |
| [2014-10-03 19:00] 7929 root 20 0 107696 2232 1240 S 0.0 0.2 0:00.00 sshd | |
| [2014-10-03 19:00] 7989 vagrant 20 0 107696 1696 700 S 0.0 0.2 0:00.36 sshd | |
| [2014-10-03 19:00] 7990 vagrant 20 0 22804 4348 856 S 0.0 0.4 0:00.12 bash | |
| [2014-10-03 19:00] 8006 root 20 0 107696 2232 1240 S 0.0 0.2 0:00.00 sshd | |
| [2014-10-03 19:00] 8059 vagrant 20 0 107696 1876 880 S 0.0 0.2 0:01.20 sshd | |
| [2014-10-03 19:00] 8060 vagrant 20 0 22804 4344 856 S 0.0 0.4 0:00.09 bash | |
| [2014-10-03 19:00] 14624 vagrant 20 0 11132 848 632 S 0.0 0.1 0:00.00 bash | |
| [2014-10-03 19:00] 14630 vagrant 20 0 109820 18008 3632 S 0.0 1.8 0:00.19 nosetests | |
| [2014-10-03 19:00] 15588 vagrant 20 0 551584 117016 15744 S 0.0 11.5 0:01.39 bcbio_nextg+ | |
| [2014-10-03 19:00] 15669 vagrant 20 0 11136 1396 1176 S 0.0 0.1 0:00.00 bash | |
| [2014-10-03 19:00] 15670 vagrant 20 0 11136 592 368 S 0.0 0.1 0:00.00 bash | |
| [2014-10-03 19:00] 15671 vagrant 20 0 11136 588 364 S 0.0 0.1 0:00.00 bash | |
| [2014-10-03 19:00] 15672 vagrant 20 0 91152 2928 2040 S 0.0 0.3 0:00.00 bamtofastq | |
| [2014-10-03 19:00] 15673 vagrant 20 0 9084 420 320 S 0.0 0.0 0:00.00 bgzip | |
| [2014-10-03 19:00] 15674 vagrant 20 0 9084 416 320 S 0.0 0.0 0:00.00 bgzip | |
| [2014-10-03 19:00] 15675 vagrant 20 0 4444 656 556 S 0.0 0.1 0:00.00 sh | |
| [2014-10-03 19:00] 15676 vagrant 20 0 23536 1392 1052 R 0.0 0.1 0:00.00 top | |
| [2014-10-03 19:00] AutoArray<unsigned long,alloc_type_cxx> failed to allocate 134217728 elements (1073741824 bytes) | |
| [2014-10-03 19:00] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/alignprep.py", line 308, in _bgzip_from_bam | |
| log_error=False) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /usr/local/bin/bamtofastq filename=/home/vagrant/bcbio-nextgen/tests/data/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam T=/home/vagrant/bcbio-nextgen/tests/test_automated_output/tmptest/bcbiotx/8d6ffbba-4b2f-11e4-93cb-080027201064/tmpBB2LWX/7_100326_FC6107FAAXX-1.fq-sort F=>(/usr/local/bin/bgzip -c /dev/stdin > /home/vagrant/bcbio-nextgen/tests/test_automated_output/tmptest/bcbiotx/8d6ffbba-4b2f-11e4-93cb-080027201064/tmpBB2LWX/7_100326_FC6107FAAXX-1.fq.gz) F2=>(/usr/local/bin/bgzip -c /dev/stdin > /home/vagrant/bcbio-nextgen/tests/test_automated_output/align_prep/7_100326_FC6107FAAXX-2.fq.gz) S=/dev/null O=/dev/null O2=/dev/null collate=1 colsbs=1073741824 | |
| 1 root 20 0 33648 2384 952 S 0.0 0.2 0:00.45 init | |
| 2 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kthreadd | |
| 3 root 20 0 0 0 0 S 0.0 0.0 0:00.20 ksoftirqd/0 | |
| 4 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kworker/0:0 | |
| 5 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kworker/0:0H | |
| 7 root 20 0 0 0 0 S 0.0 0.0 0:01.15 rcu_sched | |
| 8 root 20 0 0 0 0 S 0.0 0.0 0:02.09 rcuos/0 | |
| 9 root 20 0 0 0 0 S 0.0 0.0 0:00.00 rcu_bh | |
| 10 root 20 0 0 0 0 S 0.0 0.0 0:00.00 rcuob/0 | |
| 11 root rt 0 0 0 0 S 0.0 0.0 0:00.00 migration/0 | |
| 12 root rt 0 0 0 0 S 0.0 0.0 0:00.14 watchdog/0 | |
| 13 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 khelper | |
| 14 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kdevtmpfs | |
| 15 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 netns | |
| 16 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 writeback | |
| 17 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kintegrityd | |
| 18 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 bioset | |
| 19 root 0 -20 0 0 0 S 0.0 0.0 0:00.03 kworker/u3:0 | |
| 20 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kblockd | |
| 21 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 ata_sff | |
| 22 root 20 0 0 0 0 S 0.0 0.0 0:00.00 khubd | |
| 23 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 md | |
| 24 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 devfreq_wq | |
| 25 root 20 0 0 0 0 S 0.0 0.0 0:01.62 kworker/0:1 | |
| 26 root 20 0 0 0 0 S 0.0 0.0 0:00.00 khungtaskd | |
| 27 root 20 0 0 0 0 S 0.0 0.0 0:00.38 kswapd0 | |
| 28 root 25 5 0 0 0 S 0.0 0.0 0:00.00 ksmd | |
| 29 root 39 19 0 0 0 S 0.0 0.0 0:00.09 khugepaged | |
| 30 root 20 0 0 0 0 S 0.0 0.0 0:00.00 fsnotify_ma+ | |
| 31 root 20 0 0 0 0 S 0.0 0.0 0:00.00 ecryptfs-kt+ | |
| 32 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 crypto | |
| 44 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kthrotld | |
| 64 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 deferwq | |
| 65 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 charger_man+ | |
| 106 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kpsmoused | |
| 107 root 20 0 0 0 0 S 0.0 0.0 0:00.00 scsi_eh_0 | |
| 108 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kworker/u2:2 | |
| 109 root 20 0 0 0 0 S 0.0 0.0 0:00.93 kworker/u2:3 | |
| 154 root 20 0 0 0 0 S 0.0 0.0 0:00.22 jbd2/sda1-8 | |
| 155 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 ext4-rsv-co+ | |
| 394 root 20 0 19604 756 432 S 0.0 0.1 0:00.04 upstart-ude+ | |
| 399 root 20 0 50100 1616 680 S 0.0 0.2 0:00.05 systemd-ude+ | |
| 431 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 iprt | |
| 434 root 0 -20 0 0 0 S 0.0 0.0 0:00.05 kworker/u3:1 | |
| 521 root 20 0 23420 956 640 S 0.0 0.1 0:00.02 rpcbind | |
| 526 root 20 0 15260 300 88 S 0.0 0.0 0:00.02 upstart-soc+ | |
| 564 root 20 0 10224 2292 0 S 0.0 0.2 0:00.00 dhclient | |
| 567 statd 20 0 21544 1144 684 S 0.0 0.1 0:00.00 rpc.statd | |
| 732 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 rpciod | |
| 776 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 nfsiod | |
| 826 root 20 0 15276 524 288 S 0.0 0.1 0:00.00 upstart-fil+ | |
| 855 root 20 0 25544 308 84 S 0.0 0.0 0:00.00 rpc.idmapd | |
| 866 syslog 20 0 257912 2816 324 S 0.0 0.3 0:00.02 rsyslogd | |
| 880 message+ 20 0 39184 956 584 S 0.0 0.1 0:00.19 dbus-daemon | |
| 897 root 20 0 43452 1336 988 S 0.0 0.1 0:00.00 systemd-log+ | |
| 931 root 20 0 14540 868 704 S 0.0 0.1 0:00.00 getty | |
| 934 root 20 0 14540 856 704 S 0.0 0.1 0:00.00 getty | |
| 939 root 20 0 14540 864 704 S 0.0 0.1 0:00.00 getty | |
| 940 root 20 0 14540 864 704 S 0.0 0.1 0:00.00 getty | |
| 942 root 20 0 14540 864 704 S 0.0 0.1 0:00.00 getty | |
| 965 root 20 0 61364 1608 932 S 0.0 0.2 0:00.00 sshd | |
| 969 root 20 0 4368 556 412 S 0.0 0.1 0:00.00 acpid | |
| 997 root 20 0 23656 824 612 S 0.0 0.1 0:00.01 cron | |
| 998 daemon 20 0 19140 164 0 S 0.0 0.0 0:00.00 atd | |
| 1015 root 20 0 216612 912 588 S 0.0 0.1 0:02.12 VBoxService | |
| 1041 root 20 0 182524 32608 820 S 0.0 3.2 0:00.12 puppet | |
| 1071 root 20 0 112692 33824 384 S 0.0 3.3 0:00.00 ruby | |
| 1098 root 20 0 14540 860 700 S 0.0 0.1 0:00.00 getty | |
| 1168 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kauditd | |
| 7929 root 20 0 107696 2232 1240 S 0.0 0.2 0:00.00 sshd | |
| 7989 vagrant 20 0 107696 1696 700 S 0.0 0.2 0:00.36 sshd | |
| 7990 vagrant 20 0 22804 4348 856 S 0.0 0.4 0:00.12 bash | |
| 8006 root 20 0 107696 2232 1240 S 0.0 0.2 0:00.00 sshd | |
| 8059 vagrant 20 0 107696 1876 880 S 0.0 0.2 0:01.20 sshd | |
| 8060 vagrant 20 0 22804 4344 856 S 0.0 0.4 0:00.09 bash | |
| 14624 vagrant 20 0 11132 848 632 S 0.0 0.1 0:00.00 bash | |
| 14630 vagrant 20 0 109820 18008 3632 S 0.0 1.8 0:00.19 nosetests | |
| 15588 vagrant 20 0 551584 117016 15744 S 0.0 11.5 0:01.39 bcbio_nextg+ | |
| 15669 vagrant 20 0 11136 1396 1176 S 0.0 0.1 0:00.00 bash | |
| 15670 vagrant 20 0 11136 592 368 S 0.0 0.1 0:00.00 bash | |
| 15671 vagrant 20 0 11136 588 364 S 0.0 0.1 0:00.00 bash | |
| 15672 vagrant 20 0 91152 2928 2040 S 0.0 0.3 0:00.00 bamtofastq | |
| 15673 vagrant 20 0 9084 420 320 S 0.0 0.0 0:00.00 bgzip | |
| 15674 vagrant 20 0 9084 416 320 S 0.0 0.0 0:00.00 bgzip | |
| 15675 vagrant 20 0 4444 656 556 S 0.0 0.1 0:00.00 sh | |
| 15676 vagrant 20 0 23536 1392 1052 R 0.0 0.1 0:00.00 top | |
| AutoArray<unsigned long,alloc_type_cxx> failed to allocate 134217728 elements (1073741824 bytes) | |
| current total allocation 1074215981 | |
| /usr/local/lib/libmaus.so.0(_ZN7libmaus4util10StackTraceC1Ev+0x4c) [0x7f996a774866:??:0] | |
| /usr/local/bin/bamtofastq(_ZN7libmaus9exception16LibMausExceptionC2Ev+0x1d) [0x412873:??:?] | |
| /usr/local/bin/bamtofastq(_ZN7libmaus9autoarray9AutoArrayImLNS0_10alloc_typeE0EE13allocateArrayEm+0x79) [0x41cc45:??:?] | |
| /usr/local/bin/bamtofastq(_ZN7libmaus9autoarray9AutoArrayImLNS0_10alloc_typeE0EEC2Emb+0x27) [0x41cd95:??:?] | |
| /usr/local/bin/bamtofastq() [0x443274:??:?] | |
| /usr/local/bin/bamtofastq() [0x40ef57:??:?] | |
| /usr/local/bin/bamtofastq() [0x40feea:??:?] | |
| /usr/local/bin/bamtofastq() [0x40bde8:??:?] | |
| /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f996962fec5:??:0] | |
| /usr/local/bin/bamtofastq() [0x40d978:??:?] | |
| ' returned non-zero exit status 1 | |
| Traceback (most recent call last): | |
| File "/usr/local/bin/bcbio_nextgen.py", line 216, in <module> | |
| main(**kwargs) | |
| File "/usr/local/bin/bcbio_nextgen.py", line 42, in main | |
| run_main(**kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 36, in run_main | |
| fc_dir, run_info_yaml) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 82, in _run_toplevel | |
| for xs in pipeline.run(config, config_file, parallel, dirs, pipeline_items): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 175, in run | |
| samples = run_parallel("prep_align_inputs", samples) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel | |
| return run_multicore(fn, items, config, parallel=parallel) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 84, in run_multicore | |
| for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 653, in __call__ | |
| self.dispatch(function, args, kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 400, in dispatch | |
| job = ImmediateApply(func, args, kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 138, in __init__ | |
| self.results = func(*args, **kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 63, in wrapper | |
| return apply(f, *args, **kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 39, in prep_align_inputs | |
| return alignprep.create_inputs(*args) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/alignprep.py", line 37, in create_inputs | |
| ready_files = _prep_grabix_indexes(data["files"], data["dirs"], data) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/alignprep.py", line 153, in _prep_grabix_indexes | |
| out = _bgzip_from_bam(in_files[0], dirs, data["config"]) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/alignprep.py", line 308, in _bgzip_from_bam | |
| log_error=False) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| subprocess.CalledProcessError: Command 'set -o pipefail; /usr/local/bin/bamtofastq filename=/home/vagrant/bcbio-nextgen/tests/data/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam T=/home/vagrant/bcbio-nextgen/tests/test_automated_output/tmptest/bcbiotx/8d6ffbba-4b2f-11e4-93cb-080027201064/tmpBB2LWX/7_100326_FC6107FAAXX-1.fq-sort F=>(/usr/local/bin/bgzip -c /dev/stdin > /home/vagrant/bcbio-nextgen/tests/test_automated_output/tmptest/bcbiotx/8d6ffbba-4b2f-11e4-93cb-080027201064/tmpBB2LWX/7_100326_FC6107FAAXX-1.fq.gz) F2=>(/usr/local/bin/bgzip -c /dev/stdin > /home/vagrant/bcbio-nextgen/tests/test_automated_output/align_prep/7_100326_FC6107FAAXX-2.fq.gz) S=/dev/null O=/dev/null O2=/dev/null collate=1 colsbs=1073741824 | |
| 1 root 20 0 33648 2384 952 S 0.0 0.2 0:00.45 init | |
| 2 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kthreadd | |
| 3 root 20 0 0 0 0 S 0.0 0.0 0:00.20 ksoftirqd/0 | |
| 4 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kworker/0:0 | |
| 5 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kworker/0:0H | |
| 7 root 20 0 0 0 0 S 0.0 0.0 0:01.15 rcu_sched | |
| 8 root 20 0 0 0 0 S 0.0 0.0 0:02.09 rcuos/0 | |
| 9 root 20 0 0 0 0 S 0.0 0.0 0:00.00 rcu_bh | |
| 10 root 20 0 0 0 0 S 0.0 0.0 0:00.00 rcuob/0 | |
| 11 root rt 0 0 0 0 S 0.0 0.0 0:00.00 migration/0 | |
| 12 root rt 0 0 0 0 S 0.0 0.0 0:00.14 watchdog/0 | |
| 13 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 khelper | |
| 14 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kdevtmpfs | |
| 15 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 netns | |
| 16 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 writeback | |
| 17 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kintegrityd | |
| 18 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 bioset | |
| 19 root 0 -20 0 0 0 S 0.0 0.0 0:00.03 kworker/u3:0 | |
| 20 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kblockd | |
| 21 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 ata_sff | |
| 22 root 20 0 0 0 0 S 0.0 0.0 0:00.00 khubd | |
| 23 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 md | |
| 24 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 devfreq_wq | |
| 25 root 20 0 0 0 0 S 0.0 0.0 0:01.62 kworker/0:1 | |
| 26 root 20 0 0 0 0 S 0.0 0.0 0:00.00 khungtaskd | |
| 27 root 20 0 0 0 0 S 0.0 0.0 0:00.38 kswapd0 | |
| 28 root 25 5 0 0 0 S 0.0 0.0 0:00.00 ksmd | |
| 29 root 39 19 0 0 0 S 0.0 0.0 0:00.09 khugepaged | |
| 30 root 20 0 0 0 0 S 0.0 0.0 0:00.00 fsnotify_ma+ | |
| 31 root 20 0 0 0 0 S 0.0 0.0 0:00.00 ecryptfs-kt+ | |
| 32 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 crypto | |
| 44 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kthrotld | |
| 64 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 deferwq | |
| 65 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 charger_man+ | |
| 106 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kpsmoused | |
| 107 root 20 0 0 0 0 S 0.0 0.0 0:00.00 scsi_eh_0 | |
| 108 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kworker/u2:2 | |
| 109 root 20 0 0 0 0 S 0.0 0.0 0:00.93 kworker/u2:3 | |
| 154 root 20 0 0 0 0 S 0.0 0.0 0:00.22 jbd2/sda1-8 | |
| 155 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 ext4-rsv-co+ | |
| 394 root 20 0 19604 756 432 S 0.0 0.1 0:00.04 upstart-ude+ | |
| 399 root 20 0 50100 1616 680 S 0.0 0.2 0:00.05 systemd-ude+ | |
| 431 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 iprt | |
| 434 root 0 -20 0 0 0 S 0.0 0.0 0:00.05 kworker/u3:1 | |
| 521 root 20 0 23420 956 640 S 0.0 0.1 0:00.02 rpcbind | |
| 526 root 20 0 15260 300 88 S 0.0 0.0 0:00.02 upstart-soc+ | |
| 564 root 20 0 10224 2292 0 S 0.0 0.2 0:00.00 dhclient | |
| 567 statd 20 0 21544 1144 684 S 0.0 0.1 0:00.00 rpc.statd | |
| 732 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 rpciod | |
| 776 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 nfsiod | |
| 826 root 20 0 15276 524 288 S 0.0 0.1 0:00.00 upstart-fil+ | |
| 855 root 20 0 25544 308 84 S 0.0 0.0 0:00.00 rpc.idmapd | |
| 866 syslog 20 0 257912 2816 324 S 0.0 0.3 0:00.02 rsyslogd | |
| 880 message+ 20 0 39184 956 584 S 0.0 0.1 0:00.19 dbus-daemon | |
| 897 root 20 0 43452 1336 988 S 0.0 0.1 0:00.00 systemd-log+ | |
| 931 root 20 0 14540 868 704 S 0.0 0.1 0:00.00 getty | |
| 934 root 20 0 14540 856 704 S 0.0 0.1 0:00.00 getty | |
| 939 root 20 0 14540 864 704 S 0.0 0.1 0:00.00 getty | |
| 940 root 20 0 14540 864 704 S 0.0 0.1 0:00.00 getty | |
| 942 root 20 0 14540 864 704 S 0.0 0.1 0:00.00 getty | |
| 965 root 20 0 61364 1608 932 S 0.0 0.2 0:00.00 sshd | |
| 969 root 20 0 4368 556 412 S 0.0 0.1 0:00.00 acpid | |
| 997 root 20 0 23656 824 612 S 0.0 0.1 0:00.01 cron | |
| 998 daemon 20 0 19140 164 0 S 0.0 0.0 0:00.00 atd | |
| 1015 root 20 0 216612 912 588 S 0.0 0.1 0:02.12 VBoxService | |
| 1041 root 20 0 182524 32608 820 S 0.0 3.2 0:00.12 puppet | |
| 1071 root 20 0 112692 33824 384 S 0.0 3.3 0:00.00 ruby | |
| 1098 root 20 0 14540 860 700 S 0.0 0.1 0:00.00 getty | |
| 1168 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kauditd | |
| 7929 root 20 0 107696 2232 1240 S 0.0 0.2 0:00.00 sshd | |
| 7989 vagrant 20 0 107696 1696 700 S 0.0 0.2 0:00.36 sshd | |
| 7990 vagrant 20 0 22804 4348 856 S 0.0 0.4 0:00.12 bash | |
| 8006 root 20 0 107696 2232 1240 S 0.0 0.2 0:00.00 sshd | |
| 8059 vagrant 20 0 107696 1876 880 S 0.0 0.2 0:01.20 sshd | |
| 8060 vagrant 20 0 22804 4344 856 S 0.0 0.4 0:00.09 bash | |
| 14624 vagrant 20 0 11132 848 632 S 0.0 0.1 0:00.00 bash | |
| 14630 vagrant 20 0 109820 18008 3632 S 0.0 1.8 0:00.19 nosetests | |
| 15588 vagrant 20 0 551584 117016 15744 S 0.0 11.5 0:01.39 bcbio_nextg+ | |
| 15669 vagrant 20 0 11136 1396 1176 S 0.0 0.1 0:00.00 bash | |
| 15670 vagrant 20 0 11136 592 368 S 0.0 0.1 0:00.00 bash | |
| 15671 vagrant 20 0 11136 588 364 S 0.0 0.1 0:00.00 bash | |
| 15672 vagrant 20 0 91152 2928 2040 S 0.0 0.3 0:00.00 bamtofastq | |
| 15673 vagrant 20 0 9084 420 320 S 0.0 0.0 0:00.00 bgzip | |
| 15674 vagrant 20 0 9084 416 320 S 0.0 0.0 0:00.00 bgzip | |
| 15675 vagrant 20 0 4444 656 556 S 0.0 0.1 0:00.00 sh | |
| 15676 vagrant 20 0 23536 1392 1052 R 0.0 0.1 0:00.00 top | |
| AutoArray<unsigned long,alloc_type_cxx> failed to allocate 134217728 elements (1073741824 bytes) | |
| current total allocation 1074215981 | |
| /usr/local/lib/libmaus.so.0(_ZN7libmaus4util10StackTraceC1Ev+0x4c) [0x7f996a774866:??:0] | |
| /usr/local/bin/bamtofastq(_ZN7libmaus9exception16LibMausExceptionC2Ev+0x1d) [0x412873:??:?] | |
| /usr/local/bin/bamtofastq(_ZN7libmaus9autoarray9AutoArrayImLNS0_10alloc_typeE0EE13allocateArrayEm+0x79) [0x41cc45:??:?] | |
| /usr/local/bin/bamtofastq(_ZN7libmaus9autoarray9AutoArrayImLNS0_10alloc_typeE0EEC2Emb+0x27) [0x41cd95:??:?] | |
| /usr/local/bin/bamtofastq() [0x443274:??:?] | |
| /usr/local/bin/bamtofastq() [0x40ef57:??:?] | |
| /usr/local/bin/bamtofastq() [0x40feea:??:?] | |
| /usr/local/bin/bamtofastq() [0x40bde8:??:?] | |
| /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f996962fec5:??:0] | |
| /usr/local/bin/bamtofastq() [0x40d978:??:?] | |
| ' returned non-zero exit status 1 | |
| ERROR | |
| Create a project template from input files and metadata configuration. ... variant_regions ../data/100326_FC6107FAAXX/test.bed | |
| sex female | |
| description 7_1 | |
| batch 1a | |
| variant_regions ../data/100326_FC6107FAAXX/test.bed | |
| sex | |
| description 8_1 | |
| batch 1a | |
| Configuration file created at: /home/vagrant/bcbio-nextgen/tests/test_automated_output/100326/config/100326.yaml | |
| Edit to finalize and run with: | |
| cd /home/vagrant/bcbio-nextgen/tests/test_automated_output/100326/work | |
| bcbio_nextgen.py ../config/100326.yaml | |
| ok | |
| Identify programs and versions used in analysis. ... [{'program': 'bcbio-nextgen', 'version': '0.8.3a-9f027b9'}, {'program': 'alientrimmer', 'version': '0.3.2'}, {'program': 'bamtools', 'version': '2.3.0'}, {'program': 'bcbio_variation', 'version': '0.1.7'}, {'program': 'bcftools', 'version': '1.1'}, {'program': 'bedtools', 'version': '2.21.0'}, {'program': 'biobambam', 'version': '0.0.154'}, {'program': 'bowtie2', 'version': '2.2.3'}, {'program': 'bwa', 'version': '0.7.10'}, {'program': 'chanjo', 'version': '2.1.2'}, {'program': 'cn.mops', 'version': '1.10.1'}, {'program': 'cufflinks', 'version': '2.1.1'}, {'program': 'cutadapt', 'version': '1.4.2'}, {'program': 'fastqc', 'version': '0.11.2'}, {'program': 'featurecounts', 'version': '1.4.4'}, {'program': 'freebayes', 'version': '0.9.14-15'}, {'program': 'gatk', 'version': '3.2-2-gec30cee'}, {'program': 'gatk-framework', 'version': '3.2-4'}, {'program': 'gemini', 'version': '0.10.1'}, {'program': 'htseq', 'version': '0.6.1p1'}, {'program': 'mutect', 'version': '1.1.5'}, {'program': 'novoalign', 'version': '3.02.02'}, {'program': 'novosort', 'version': 'V3.00.02'}, {'program': 'oncofuse', 'version': '1.0.7'}, {'program': 'picard', 'version': '1.96'}, {'program': 'platypus-variant', 'version': '0.7.9.2'}, {'program': 'qualimap', 'version': '0.7.1'}, {'program': 'rnaseqc', 'version': '1.1.7'}, {'program': 'sambamba', 'version': '0.4.7'}, {'program': 'samtools', 'version': '1.1'}, {'program': 'snpeff', 'version': '3.6c'}, {'program': 'tophat', 'version': '2.0.9'}, {'program': 'varscan', 'version': '2.3.7'}, {'program': 'vcflib', 'version': '2014-09-29'}, {'program': 'vt', 'version': '2014-09-25'}] | |
| ok | |
| Parallel combination of VCF files, split by chromosome. ... [2014-10-03 19:00] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: bgzip S1-variants.vcf | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bgzip -c /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants.vcf > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpurjGbV/S1-variants.vcf.gz | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: tabix index S1-variants.vcf.gz | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpAGlMQZ/S1-variants.vcf.gz | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: bgzip S2-variants.vcf | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bgzip -c /home/vagrant/bcbio-nextgen/tests/data/variants/S2-variants.vcf > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpvt7VZm/S2-variants.vcf.gz | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: tabix index S2-variants.vcf.gz | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmp5b4_Z9/S2-variants.vcf.gz | |
| [2014-10-03 19:00] INFO: bcbio-nextgen: multiprocessing: merge_variant_files | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: Merge variants | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bcftools merge -O z -r chrM `cat /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/S1_S2-combined-chrM-files.txt` > /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/tx/tmp7F_FNb/S1_S2-combined-chrM.vcf.gz | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: tabix index S1_S2-combined-chrM.vcf.gz | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/tx/tmp4RNHge/S1_S2-combined-chrM.vcf.gz | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: Merge variants | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bcftools merge -O z -r chr22 `cat /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/S1_S2-combined-chr22-files.txt` > /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/tx/tmpAog0oe/S1_S2-combined-chr22.vcf.gz | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: tabix index S1_S2-combined-chr22.vcf.gz | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/tx/tmpL6WQio/S1_S2-combined-chr22.vcf.gz | |
| [2014-10-03 19:00] INFO: bcbio-nextgen: multiprocessing: concat_variant_files | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: Concat variant files | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen-commands: /usr/local/bin/gatk-framework org.broadinstitute.gatk.tools.CatVariants -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -V /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-files.list -out /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpVKWHGf/S1_S2-combined.vcf.gz -assumeSorted -Xms500m -Xmx3500m -XX:+UseSerialGC | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:44,924 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:44,926 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:44,929 HelpFormatter - Program Args: -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -V /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-files.list -out /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpVKWHGf/S1_S2-combined.vcf.gz -assumeSorted | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:44,939 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:44,940 HelpFormatter - Date/Time: 2014/10/03 19:00:44 | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:44,940 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:44,941 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: .. | |
| ok | |
| Exclude samples from VCF files. ... [2014-10-03 19:00] DEBUG: bcbio-nextgen: Exclude samples: ['S1'] | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bcftools view -O z -s S2 /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined.vcf.gz > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmp7Fdhhq/S1_S2-combined-exclude.vcf.gz | |
| ok | |
| Split a VCF file into SNPs and indels, then combine back together. ... [2014-10-03 19:00] DEBUG: bcbio-nextgen: Subset to SNPs and indels | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bcftools view -O v /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants.vcf --types snps > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpfslTYs/S1-variants-snp.vcf | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: Subset to SNPs and indels | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bcftools view -O v /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants.vcf --exclude-types snps > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpQuxZO0/S1-variants-indel.vcf | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: bgzip S1-variants-snp.vcf | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bgzip -c /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants-snp.vcf > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmp_ofzZI/S1-variants-snp.vcf.gz | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: tabix index S1-variants-snp.vcf.gz | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpfJlneu/S1-variants-snp.vcf.gz | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: bgzip S1-variants-indel.vcf | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bgzip -c /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants-indel.vcf > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpxHdMIF/S1-variants-indel.vcf.gz | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: tabix index S1-variants-indel.vcf.gz | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpf10jJL/S1-variants-indel.vcf.gz | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: Combine variant files | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen-commands: /usr/local/bin/gatk-framework -Xms500m -Xmx3500m -XX:+UseSerialGC -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --out /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpHb1CLQ/S1-variants-merge.vcf.gz --variant:v0 /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants-snp.vcf.gz --variant:v1 /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants-indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:46,997 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:46,999 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53 | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:47,000 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:47,000 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:47,002 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --out /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpHb1CLQ/S1-variants-merge.vcf.gz --variant:v0 /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants-snp.vcf.gz --variant:v1 /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants-indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:47,005 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:47,005 HelpFormatter - Date/Time: 2014/10/03 19:00:46 | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:47,006 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:47,006 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:47,485 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:47,528 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: WARN 19:00:47,563 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: WARN 19:00:47,571 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:47,621 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:47,622 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:47,623 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:47,624 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:47,625 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:47,700 ProgressMeter - done 12.0 0.0 s 103.0 m 45.7% 0.0 s 0.0 s | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: INFO 19:00:47,701 ProgressMeter - Total runtime 0.08 secs, 0.00 min, 0.00 hours | |
| ok | |
| Select a sample from a VCF file. ... [2014-10-03 19:00] DEBUG: bcbio-nextgen: Select sample: S2 | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bcftools view -O z /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined.vcf.gz -s S2 > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpslKoDq/S1_S2-combined-sampleselect.vcf.gz | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen: tabix index S1_S2-combined-sampleselect.vcf.gz | |
| [2014-10-03 19:00] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpdIJY4e/S1_S2-combined-sampleselect.vcf.gz | |
| ok | |
| Ensure we can correctly find paired fastq files. ... ok | |
| ====================================================================== | |
| ERROR: Allow BAM files as input to pipeline. | |
| ---------------------------------------------------------------------- | |
| Traceback (most recent call last): | |
| File "/home/vagrant/bcbio-nextgen/tests/test_automated_analysis.py", line 261, in test_5_bam | |
| subprocess.check_call(cl) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/subprocess.py", line 540, in check_call | |
| raise CalledProcessError(retcode, cmd) | |
| CalledProcessError: Command '['bcbio_nextgen.py', '/home/vagrant/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml', '/home/vagrant/bcbio-nextgen/tests/data/automated/run_info-bam.yaml']' returned non-zero exit status 1 | |
| ---------------------------------------------------------------------- | |
| Ran 11 tests in 227.987s | |
| FAILED (errors=1) | |
| vagrant@vagrant-ubuntu-trusty-64:~/bcbio-nextgen/tests$ exit | |
| logout | |
| Connection to 127.0.0.1 closed. | |
| christophes-pro:bcbio pfaucon$ vagrant halt | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| ==> default: Attempting graceful shutdown of VM... | |
| christophes-pro:bcbio pfaucon$ nano Vagrantfile | |
| christophes-pro:bcbio pfaucon$ vagrant up | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| Bringing machine 'default' up with 'virtualbox' provider... | |
| ==> default: Checking if box 'ubuntu/trusty64' is up to date... | |
| ==> default: Clearing any previously set forwarded ports... | |
| ==> default: Clearing any previously set network interfaces... | |
| ==> default: Preparing network interfaces based on configuration... | |
| default: Adapter 1: nat | |
| ==> default: Forwarding ports... | |
| default: 8090 => 8090 (adapter 1) | |
| default: 22 => 2222 (adapter 1) | |
| ==> default: Running 'pre-boot' VM customizations... | |
| ==> default: Booting VM... | |
| ==> default: Waiting for machine to boot. This may take a few minutes... | |
| default: SSH address: 127.0.0.1:2222 | |
| default: SSH username: vagrant | |
| default: SSH auth method: private key | |
| default: Warning: Connection timeout. Retrying... | |
| ==> default: Machine booted and ready! | |
| ==> default: Checking for guest additions in VM... | |
| ==> default: Mounting shared folders... | |
| default: /vagrant => /Volumes/WORK/vagrant/bcbio | |
| default: /vagrant_data => /Volumes/WORK/rnaseq | |
| ==> default: Machine already provisioned. Run `vagrant provision` or use the `--provision` | |
| ==> default: to force provisioning. Provisioners marked to run always will still run. | |
| christophes-pro:bcbio pfaucon$ vagrant ssh | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| Welcome to Ubuntu 14.04.1 LTS (GNU/Linux 3.13.0-35-generic x86_64) | |
| * Documentation: https://help.ubuntu.com/ | |
| System information as of Fri Oct 3 19:03:14 UTC 2014 | |
| System load: 0.74 Processes: 84 | |
| Usage of /: 73.8% of 39.34GB Users logged in: 0 | |
| Memory usage: 1% IP address for eth0: 10.0.2.15 | |
| Swap usage: 0% | |
| Graph this data and manage this system at: | |
| https://landscape.canonical.com/ | |
| Get cloud support with Ubuntu Advantage Cloud Guest: | |
| http://www.ubuntu.com/business/services/cloud | |
| Last login: Fri Oct 3 17:16:33 2014 from 10.0.2.2 | |
| vagrant@vagrant-ubuntu-trusty-64:~$ cd | |
| .ant/ .cache/ .continuum/ gatk/ .java/ .m2/ tmp/ | |
| bcbio-nextgen/ .config/ .cpanm/ gatk2/ Library/ .ssh/ | |
| vagrant@vagrant-ubuntu-trusty-64:~$ cd bcbio-nextgen/tests/ | |
| vagrant@vagrant-ubuntu-trusty-64:~/bcbio-nextgen/tests$ ./run_tests.sh | |
| Check for the presence of runs in an Illumina SampleSheet. ... ok | |
| Convert CSV Illumina SampleSheet to YAML. ... ok | |
| Test variant calling with GATK pipeline. ... [2014-10-03 19:03] Using input YAML configuration: /home/vagrant/bcbio-nextgen/tests/data/automated/run_info-variantcall.yaml | |
| [2014-10-03 19:03] Checking sample YAML configuration: /home/vagrant/bcbio-nextgen/tests/data/automated/run_info-variantcall.yaml | |
| [2014-10-03 19:03] Testing minimum versions of installed programs | |
| [2014-10-03 19:03] Resource requests: novoalign, sambamba, samtools; memory: 2.0, 2.0; cores: 16, 1, 16 | |
| [2014-10-03 19:03] Configuring 1 jobs to run, using 1 cores each with 2.2g of memory reserved for each job | |
| [2014-10-03 19:03] Timing: alignment preparation | |
| [2014-10-03 19:03] multiprocessing: prep_align_inputs | |
| [2014-10-03 19:03] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:03] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:03] bgzip input file | |
| [2014-10-03 19:03] bgzip input file | |
| [2014-10-03 19:03] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:03] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:03] Index input with grabix: 7_100326_FC6107FAAXX_1_fastq.txt.gz | |
| [2014-10-03 19:03] Index input with grabix: 7_100326_FC6107FAAXX_2_fastq.txt.gz | |
| [2014-10-03 19:03] Timing: alignment | |
| [2014-10-03 19:03] multiprocessing: process_alignment | |
| [2014-10-03 19:03] Aligning lane 7_100326_FC6107FAAXX with novoalign aligner | |
| [2014-10-03 19:03] Novoalign: Test1 | |
| [2014-10-03 19:03] samblaster: Version 0.1.20 | |
| [2014-10-03 19:03] samblaster: Inputting from stdin | |
| [2014-10-03 19:03] samblaster: Outputting to stdout | |
| [2014-10-03 19:03] samblaster: Opening /dev/fd/62 for write. | |
| [2014-10-03 19:03] samblaster: Opening /dev/fd/63 for write. | |
| [2014-10-03 19:03] Command line argument ignored: -c option is only available in licensed versions. at '-c' | |
| [2014-10-03 19:03] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 19:03] Command line argument ignored: -k option is only available in licensed versions. at '-k' | |
| [2014-10-03 19:03] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 19:03] # novoalign (V3.02.02 - Build Feb 4 2014 @ 15:23:48 - A short read aligner with qualities. | |
| [2014-10-03 19:03] # (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd. | |
| [2014-10-03 19:03] # License file not found. | |
| [2014-10-03 19:03] # Licensed for evaluation, educational, and not-for-profit use only. | |
| [2014-10-03 19:03] # novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 19:03] # Starting at Fri Oct 3 19:03:46 2014 | |
| [2014-10-03 19:03] # Interpreting input files as Sanger FASTQ. | |
| [2014-10-03 19:03] # Index Build Version: 2.7 | |
| [2014-10-03 19:03] # Hash length: 6 | |
| [2014-10-03 19:03] # Step size: 1 | |
| [2014-10-03 19:03] samblaster: Loaded 2 header sequence entries. | |
| [2014-10-03 19:03] # Paired Reads: 9000 | |
| [2014-10-03 19:03] # Pairs Aligned: 8889 | |
| [2014-10-03 19:03] # Read Sequences: 18000 | |
| [2014-10-03 19:03] # Aligned: 17874 | |
| [2014-10-03 19:03] # Unique Alignment: 17874 | |
| [2014-10-03 19:03] # Gapped Alignment: 67 | |
| [2014-10-03 19:03] # Quality Filter: 126 | |
| [2014-10-03 19:03] # Homopolymer Filter: 0 | |
| [2014-10-03 19:03] # Elapsed Time: 2.536 (secs.) | |
| [2014-10-03 19:03] # CPU Time: 2.38 (secs.) | |
| [2014-10-03 19:03] # Fragment Length Distribution | |
| [2014-10-03 19:03] # From To Count | |
| [2014-10-03 19:03] # 60 74 9 | |
| [2014-10-03 19:03] # 75 89 197 | |
| [2014-10-03 19:03] # 90 104 300 | |
| [2014-10-03 19:03] # 105 119 628 | |
| [2014-10-03 19:03] # 120 134 1584 | |
| [2014-10-03 19:03] # 135 149 1604 | |
| [2014-10-03 19:03] # 150 164 1419 | |
| [2014-10-03 19:03] # 165 179 1258 | |
| [2014-10-03 19:03] # 180 194 967 | |
| [2014-10-03 19:03] # 195 209 677 | |
| [2014-10-03 19:03] # 210 224 223 | |
| [2014-10-03 19:03] # 225 239 21 | |
| [2014-10-03 19:03] # 240 254 2 | |
| [2014-10-03 19:03] # Mean 153, Std Dev 31.1 | |
| [2014-10-03 19:03] # Done at Fri Oct 3 19:03:48 2014 | |
| [2014-10-03 19:03] samblaster: Output 0 discordant read pairs to /dev/fd/62 | |
| [2014-10-03 19:03] samblaster: Output 0 split reads to /dev/fd/63 | |
| [2014-10-03 19:03] samblaster: Marked 97 of 9000 (1.08%) read ids as duplicates using 1332k memory in 0.020S CPU seconds and 2S wall time. | |
| [2014-10-03 19:03] Index BAM file: 7_100326_FC6107FAAXX-sort-1_36000.bam | |
| [2014-10-03 19:03] Index BAM file: 7_100326_FC6107FAAXX-sort-1_36000-sr.bam | |
| [2014-10-03 19:03] Index BAM file: 7_100326_FC6107FAAXX-sort-1_36000-disc.bam | |
| [2014-10-03 19:03] Aligning lane 7_100326_FC6107FAAXX with novoalign aligner | |
| [2014-10-03 19:03] Novoalign: Test1 | |
| [2014-10-03 19:03] samblaster: Version 0.1.20 | |
| [2014-10-03 19:03] samblaster: Inputting from stdin | |
| [2014-10-03 19:03] samblaster: Outputting to stdout | |
| [2014-10-03 19:03] samblaster: Opening /dev/fd/62 for write. | |
| [2014-10-03 19:03] samblaster: Opening /dev/fd/63 for write. | |
| [2014-10-03 19:03] Command line argument ignored: -c option is only available in licensed versions. at '-c' | |
| [2014-10-03 19:03] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 19:03] Command line argument ignored: -k option is only available in licensed versions. at '-k' | |
| [2014-10-03 19:03] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 19:03] # novoalign (V3.02.02 - Build Feb 4 2014 @ 15:23:48 - A short read aligner with qualities. | |
| [2014-10-03 19:03] # (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd. | |
| [2014-10-03 19:03] # License file not found. | |
| [2014-10-03 19:03] # Licensed for evaluation, educational, and not-for-profit use only. | |
| [2014-10-03 19:03] # novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 19:03] # Starting at Fri Oct 3 19:03:49 2014 | |
| [2014-10-03 19:03] # Interpreting input files as Sanger FASTQ. | |
| [2014-10-03 19:03] # Index Build Version: 2.7 | |
| [2014-10-03 19:03] # Hash length: 6 | |
| [2014-10-03 19:03] # Step size: 1 | |
| [2014-10-03 19:03] samblaster: Loaded 2 header sequence entries. | |
| [2014-10-03 19:03] # Paired Reads: 9000 | |
| [2014-10-03 19:03] # Pairs Aligned: 8899 | |
| [2014-10-03 19:03] # Read Sequences: 18000 | |
| [2014-10-03 19:03] # Aligned: 17888 | |
| [2014-10-03 19:03] # Unique Alignment: 17888 | |
| [2014-10-03 19:03] # Gapped Alignment: 48 | |
| [2014-10-03 19:03] # Quality Filter: 112 | |
| [2014-10-03 19:03] # Homopolymer Filter: 0 | |
| [2014-10-03 19:03] # Elapsed Time: 2.514 (secs.) | |
| [2014-10-03 19:03] # CPU Time: 2.36 (secs.) | |
| [2014-10-03 19:03] # Fragment Length Distribution | |
| [2014-10-03 19:03] # From To Count | |
| [2014-10-03 19:03] # 60 74 5 | |
| [2014-10-03 19:03] # 75 89 195 | |
| [2014-10-03 19:03] # 90 104 308 | |
| [2014-10-03 19:03] # 105 119 669 | |
| [2014-10-03 19:03] # 120 134 1511 | |
| [2014-10-03 19:03] # 135 149 1656 | |
| [2014-10-03 19:03] # 150 164 1379 | |
| [2014-10-03 19:03] # 165 179 1207 | |
| [2014-10-03 19:03] # 180 194 1020 | |
| [2014-10-03 19:03] # 195 209 692 | |
| [2014-10-03 19:03] # 210 224 231 | |
| [2014-10-03 19:03] # 225 239 19 | |
| [2014-10-03 19:03] # 240 254 4 | |
| [2014-10-03 19:03] # 255 269 2 | |
| [2014-10-03 19:03] # 270 284 1 | |
| [2014-10-03 19:03] # Mean 153, Std Dev 31.4 | |
| [2014-10-03 19:03] # Done at Fri Oct 3 19:03:51 2014 | |
| [2014-10-03 19:03] samblaster: Output 1 discordant read pairs to /dev/fd/62 | |
| [2014-10-03 19:03] samblaster: Output 0 split reads to /dev/fd/63 | |
| [2014-10-03 19:03] samblaster: Marked 105 of 9000 (1.17%) read ids as duplicates using 1328k memory in 0.018S CPU seconds and 2S wall time. | |
| [2014-10-03 19:03] Index BAM file: 7_100326_FC6107FAAXX-sort-36000_71999.bam | |
| [2014-10-03 19:03] Index BAM file: 7_100326_FC6107FAAXX-sort-36000_71999-sr.bam | |
| [2014-10-03 19:03] Index BAM file: 7_100326_FC6107FAAXX-sort-36000_71999-disc.bam | |
| [2014-10-03 19:03] Aligning lane 7_100326_FC6107FAAXX with novoalign aligner | |
| [2014-10-03 19:03] Novoalign: Test1 | |
| [2014-10-03 19:03] samblaster: Version 0.1.20 | |
| [2014-10-03 19:03] samblaster: Inputting from stdin | |
| [2014-10-03 19:03] samblaster: Outputting to stdout | |
| [2014-10-03 19:03] samblaster: Opening /dev/fd/62 for write. | |
| [2014-10-03 19:03] samblaster: Opening /dev/fd/63 for write. | |
| [2014-10-03 19:03] Command line argument ignored: -c option is only available in licensed versions. at '-c' | |
| [2014-10-03 19:03] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 19:03] Command line argument ignored: -k option is only available in licensed versions. at '-k' | |
| [2014-10-03 19:03] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 19:03] # novoalign (V3.02.02 - Build Feb 4 2014 @ 15:23:48 - A short read aligner with qualities. | |
| [2014-10-03 19:03] # (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd. | |
| [2014-10-03 19:03] # License file not found. | |
| [2014-10-03 19:03] # Licensed for evaluation, educational, and not-for-profit use only. | |
| [2014-10-03 19:03] # novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 19:03] # Starting at Fri Oct 3 19:03:51 2014 | |
| [2014-10-03 19:03] # Interpreting input files as Sanger FASTQ. | |
| [2014-10-03 19:03] # Index Build Version: 2.7 | |
| [2014-10-03 19:03] # Hash length: 6 | |
| [2014-10-03 19:03] # Step size: 1 | |
| [2014-10-03 19:03] samblaster: Loaded 2 header sequence entries. | |
| [2014-10-03 19:03] # Paired Reads: 9000 | |
| [2014-10-03 19:03] # Pairs Aligned: 8881 | |
| [2014-10-03 19:03] # Read Sequences: 18000 | |
| [2014-10-03 19:03] # Aligned: 17872 | |
| [2014-10-03 19:03] # Unique Alignment: 17872 | |
| [2014-10-03 19:03] # Gapped Alignment: 53 | |
| [2014-10-03 19:03] # Quality Filter: 128 | |
| [2014-10-03 19:03] # Homopolymer Filter: 0 | |
| [2014-10-03 19:03] # Elapsed Time: 2.535 (secs.) | |
| [2014-10-03 19:03] # CPU Time: 2.38 (secs.) | |
| [2014-10-03 19:03] # Fragment Length Distribution | |
| [2014-10-03 19:03] # From To Count | |
| [2014-10-03 19:03] # 60 74 5 | |
| [2014-10-03 19:03] # 75 89 194 | |
| [2014-10-03 19:03] # 90 104 304 | |
| [2014-10-03 19:03] # 105 119 695 | |
| [2014-10-03 19:03] # 120 134 1547 | |
| [2014-10-03 19:03] # 135 149 1598 | |
| [2014-10-03 19:03] # 150 164 1399 | |
| [2014-10-03 19:03] # 165 179 1229 | |
| [2014-10-03 19:03] # 180 194 1010 | |
| [2014-10-03 19:03] # 195 209 669 | |
| [2014-10-03 19:03] # 210 224 202 | |
| [2014-10-03 19:03] # 225 239 24 | |
| [2014-10-03 19:03] # 240 254 2 | |
| [2014-10-03 19:03] # 255 269 2 | |
| [2014-10-03 19:03] # 270 284 1 | |
| [2014-10-03 19:03] # Mean 152, Std Dev 31.2 | |
| [2014-10-03 19:03] # Done at Fri Oct 3 19:03:54 2014 | |
| [2014-10-03 19:03] samblaster: Output 0 discordant read pairs to /dev/fd/62 | |
| [2014-10-03 19:03] samblaster: Output 0 split reads to /dev/fd/63 | |
| [2014-10-03 19:03] samblaster: Marked 105 of 9000 (1.17%) read ids as duplicates using 1332k memory in 0.007S CPU seconds and 3S wall time. | |
| [2014-10-03 19:03] Index BAM file: 7_100326_FC6107FAAXX-sort-72000_107999.bam | |
| [2014-10-03 19:03] Index BAM file: 7_100326_FC6107FAAXX-sort-72000_107999-sr.bam | |
| [2014-10-03 19:03] Index BAM file: 7_100326_FC6107FAAXX-sort-72000_107999-disc.bam | |
| [2014-10-03 19:03] Aligning lane 7_100326_FC6107FAAXX with novoalign aligner | |
| [2014-10-03 19:03] Novoalign: Test1 | |
| [2014-10-03 19:03] samblaster: Version 0.1.20 | |
| [2014-10-03 19:03] samblaster: Inputting from stdin | |
| [2014-10-03 19:03] samblaster: Outputting to stdout | |
| [2014-10-03 19:03] samblaster: Opening /dev/fd/62 for write. | |
| [2014-10-03 19:03] samblaster: Opening /dev/fd/63 for write. | |
| [2014-10-03 19:03] Command line argument ignored: -c option is only available in licensed versions. at '-c' | |
| [2014-10-03 19:03] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 19:03] Command line argument ignored: -k option is only available in licensed versions. at '-k' | |
| [2014-10-03 19:03] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 19:03] # novoalign (V3.02.02 - Build Feb 4 2014 @ 15:23:48 - A short read aligner with qualities. | |
| [2014-10-03 19:03] # (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd. | |
| [2014-10-03 19:03] # License file not found. | |
| [2014-10-03 19:03] # Licensed for evaluation, educational, and not-for-profit use only. | |
| [2014-10-03 19:03] # novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 19:03] # Starting at Fri Oct 3 19:03:54 2014 | |
| [2014-10-03 19:03] # Interpreting input files as Sanger FASTQ. | |
| [2014-10-03 19:03] # Index Build Version: 2.7 | |
| [2014-10-03 19:03] # Hash length: 6 | |
| [2014-10-03 19:03] # Step size: 1 | |
| [2014-10-03 19:03] samblaster: Loaded 2 header sequence entries. | |
| [2014-10-03 19:03] # Paired Reads: 9000 | |
| [2014-10-03 19:03] # Pairs Aligned: 8907 | |
| [2014-10-03 19:03] # Read Sequences: 18000 | |
| [2014-10-03 19:03] # Aligned: 17899 | |
| [2014-10-03 19:03] # Unique Alignment: 17899 | |
| [2014-10-03 19:03] # Gapped Alignment: 58 | |
| [2014-10-03 19:03] # Quality Filter: 101 | |
| [2014-10-03 19:03] # Homopolymer Filter: 0 | |
| [2014-10-03 19:03] # Elapsed Time: 2.513 (secs.) | |
| [2014-10-03 19:03] # CPU Time: 2.37 (secs.) | |
| [2014-10-03 19:03] # Fragment Length Distribution | |
| [2014-10-03 19:03] # From To Count | |
| [2014-10-03 19:03] # 60 74 5 | |
| [2014-10-03 19:03] # 75 89 203 | |
| [2014-10-03 19:03] # 90 104 351 | |
| [2014-10-03 19:03] # 105 119 680 | |
| [2014-10-03 19:03] # 120 134 1579 | |
| [2014-10-03 19:03] # 135 149 1551 | |
| [2014-10-03 19:03] # 150 164 1378 | |
| [2014-10-03 19:03] # 165 179 1255 | |
| [2014-10-03 19:03] # 180 194 984 | |
| [2014-10-03 19:03] # 195 209 684 | |
| [2014-10-03 19:03] # 210 224 203 | |
| [2014-10-03 19:03] # 225 239 27 | |
| [2014-10-03 19:03] # 240 254 6 | |
| [2014-10-03 19:03] # 255 269 1 | |
| [2014-10-03 19:03] # Mean 152, Std Dev 31.6 | |
| [2014-10-03 19:03] # Done at Fri Oct 3 19:03:57 2014 | |
| [2014-10-03 19:03] samblaster: Output 0 discordant read pairs to /dev/fd/62 | |
| [2014-10-03 19:03] samblaster: Output 0 split reads to /dev/fd/63 | |
| [2014-10-03 19:03] samblaster: Marked 106 of 9000 (1.18%) read ids as duplicates using 1328k memory in 0.015S CPU seconds and 3S wall time. | |
| [2014-10-03 19:03] Index BAM file: 7_100326_FC6107FAAXX-sort-108000_143999.bam | |
| [2014-10-03 19:03] Index BAM file: 7_100326_FC6107FAAXX-sort-108000_143999-sr.bam | |
| [2014-10-03 19:03] Index BAM file: 7_100326_FC6107FAAXX-sort-108000_143999-disc.bam | |
| [2014-10-03 19:03] Aligning lane 7_100326_FC6107FAAXX with novoalign aligner | |
| [2014-10-03 19:03] Novoalign: Test1 | |
| [2014-10-03 19:03] samblaster: Version 0.1.20 | |
| [2014-10-03 19:03] samblaster: Inputting from stdin | |
| [2014-10-03 19:03] samblaster: Outputting to stdout | |
| [2014-10-03 19:03] samblaster: Opening /dev/fd/62 for write. | |
| [2014-10-03 19:03] samblaster: Opening /dev/fd/63 for write. | |
| [2014-10-03 19:03] Command line argument ignored: -c option is only available in licensed versions. at '-c' | |
| [2014-10-03 19:03] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 19:03] Command line argument ignored: -k option is only available in licensed versions. at '-k' | |
| [2014-10-03 19:03] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 19:03] # novoalign (V3.02.02 - Build Feb 4 2014 @ 15:23:48 - A short read aligner with qualities. | |
| [2014-10-03 19:03] # (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd. | |
| [2014-10-03 19:03] # License file not found. | |
| [2014-10-03 19:03] # Licensed for evaluation, educational, and not-for-profit use only. | |
| [2014-10-03 19:03] # novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 19:03] # Starting at Fri Oct 3 19:03:57 2014 | |
| [2014-10-03 19:03] # Interpreting input files as Sanger FASTQ. | |
| [2014-10-03 19:03] # Index Build Version: 2.7 | |
| [2014-10-03 19:03] # Hash length: 6 | |
| [2014-10-03 19:03] # Step size: 1 | |
| [2014-10-03 19:03] samblaster: Loaded 2 header sequence entries. | |
| [2014-10-03 19:03] # Paired Reads: 4164 | |
| [2014-10-03 19:03] # Pairs Aligned: 4099 | |
| [2014-10-03 19:03] # Read Sequences: 8328 | |
| [2014-10-03 19:03] # Aligned: 8231 | |
| [2014-10-03 19:03] # Unique Alignment: 8231 | |
| [2014-10-03 19:03] # Gapped Alignment: 57 | |
| [2014-10-03 19:03] # Quality Filter: 28 | |
| [2014-10-03 19:03] # Homopolymer Filter: 0 | |
| [2014-10-03 19:03] # Elapsed Time: 1.230 (secs.) | |
| [2014-10-03 19:03] # CPU Time: 1.15 (secs.) | |
| [2014-10-03 19:03] # Fragment Length Distribution | |
| [2014-10-03 19:03] # From To Count | |
| [2014-10-03 19:03] # 60 74 2 | |
| [2014-10-03 19:03] # 75 89 84 | |
| [2014-10-03 19:03] # 90 104 151 | |
| [2014-10-03 19:03] # 105 119 311 | |
| [2014-10-03 19:03] # 120 134 693 | |
| [2014-10-03 19:03] # 135 149 757 | |
| [2014-10-03 19:03] # 150 164 667 | |
| [2014-10-03 19:03] # 165 179 544 | |
| [2014-10-03 19:03] # 180 194 426 | |
| [2014-10-03 19:03] # 195 209 310 | |
| [2014-10-03 19:03] # 210 224 112 | |
| [2014-10-03 19:03] # 225 239 16 | |
| [2014-10-03 19:03] # 240 254 14 | |
| [2014-10-03 19:03] # 255 269 1 | |
| [2014-10-03 19:03] # 270 284 1 | |
| [2014-10-03 19:03] # 285 299 1 | |
| [2014-10-03 19:03] # 300 314 3 | |
| [2014-10-03 19:03] # 315 329 0 | |
| [2014-10-03 19:03] # 330 344 1 | |
| [2014-10-03 19:03] # 345 359 0 | |
| [2014-10-03 19:03] # 360 374 0 | |
| [2014-10-03 19:03] # 375 389 1 | |
| [2014-10-03 19:03] # 390 404 0 | |
| [2014-10-03 19:03] # 405 419 0 | |
| [2014-10-03 19:03] # 420 434 0 | |
| [2014-10-03 19:03] # 435 449 0 | |
| [2014-10-03 19:03] # 450 464 0 | |
| [2014-10-03 19:03] # 465 479 0 | |
| [2014-10-03 19:03] # 480 494 0 | |
| [2014-10-03 19:03] # 495 509 1 | |
| [2014-10-03 19:03] # Mean 153, Std Dev 32.9 | |
| [2014-10-03 19:03] # Done at Fri Oct 3 19:03:58 2014 | |
| [2014-10-03 19:03] samblaster: Output 3 discordant read pairs to /dev/fd/62 | |
| [2014-10-03 19:03] samblaster: Output 0 split reads to /dev/fd/63 | |
| [2014-10-03 19:03] samblaster: Marked 31 of 4164 (0.74%) read ids as duplicates using 1332k memory in 0.008S CPU seconds and 1S wall time. | |
| [2014-10-03 19:03] Index BAM file: 7_100326_FC6107FAAXX-sort-144000_160655.bam | |
| [2014-10-03 19:03] Index BAM file: 7_100326_FC6107FAAXX-sort-144000_160655-sr.bam | |
| [2014-10-03 19:03] Index BAM file: 7_100326_FC6107FAAXX-sort-144000_160655-disc.bam | |
| [2014-10-03 19:03] multiprocessing: delayed_bam_merge | |
| [2014-10-03 19:03] Merge bam files to 7_100326_FC6107FAAXX-sort-sr.bam | |
| [2014-10-03 19:03] Index BAM file: 7_100326_FC6107FAAXX-sort-sr.bam | |
| [2014-10-03 19:03] Merge bam files to 7_100326_FC6107FAAXX-sort-disc.bam | |
| [2014-10-03 19:03] Index BAM file: 7_100326_FC6107FAAXX-sort-disc.bam | |
| [2014-10-03 19:03] Merge bam files to 7_100326_FC6107FAAXX-sort.bam | |
| [2014-10-03 19:03] Index BAM file: 7_100326_FC6107FAAXX-sort.bam | |
| [2014-10-03 19:03] Timing: callable regions | |
| [2014-10-03 19:03] multiprocessing: prep_samples | |
| [2014-10-03 19:03] Prepare cleaned BED file : Test1 | |
| [2014-10-03 19:03] bgzip variant_regions-variantcall.bed | |
| [2014-10-03 19:03] tabix index variant_regions-variantcall.bed.gz | |
| [2014-10-03 19:03] Prepare merged BED file : Test1 | |
| [2014-10-03 19:03] bgzip variant_regions-variantcall-merged.bed | |
| [2014-10-03 19:03] tabix index variant_regions-variantcall-merged.bed.gz | |
| [2014-10-03 19:03] multiprocessing: postprocess_alignment | |
| [2014-10-03 19:03] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:03] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:03] multiprocessing: calc_callable_loci | |
| [2014-10-03 19:03] bedtools genomecov: chrM : 7_100326_FC6107FAAXX-sort.bam | |
| [2014-10-03 19:04] bedtools genomecov: chr22 : 7_100326_FC6107FAAXX-sort.bam | |
| [2014-10-03 19:04] multiprocessing: combine_bed | |
| [2014-10-03 19:04] Recalibrating ['', 'Test1'] with GATK | |
| [2014-10-03 19:04] GATK: BaseRecalibrator | |
| [2014-10-03 19:04] INFO 19:04:01,982 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:01,985 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 19:04] INFO 19:04:01,985 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:04] INFO 19:04:01,986 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:04] INFO 19:04:01,990 HelpFormatter - Program Args: -T BaseRecalibrator -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/tx/tmp8RLAZv/7_100326_FC6107FAAXX-sort.grp -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.bam -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --knownSites /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-variantcall.bed --interval_set_rule INTERSECTION -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment | |
| [2014-10-03 19:04] INFO 19:04:01,993 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:04] INFO 19:04:01,994 HelpFormatter - Date/Time: 2014/10/03 19:04:01 | |
| [2014-10-03 19:04] INFO 19:04:01,995 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:01,995 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:02,572 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:04] INFO 19:04:02,674 GenomeAnalysisEngine - Downsampling Settings: No downsampling | |
| [2014-10-03 19:04] INFO 19:04:02,681 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 19:04] INFO 19:04:02,695 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 19:04] INFO 19:04:02,728 IntervalUtils - Processing 5650 bp from intervals | |
| [2014-10-03 19:04] WARN 19:04:02,730 IndexDictionaryUtils - Track knownSites doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:04] INFO 19:04:02,792 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 19:04] INFO 19:04:02,808 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:04] INFO 19:04:02,809 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:04] INFO 19:04:02,810 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 19:04] INFO 19:04:02,810 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime | |
| [2014-10-03 19:04] INFO 19:04:02,841 BaseRecalibrator - The covariates being used here: | |
| [2014-10-03 19:04] INFO 19:04:02,842 BaseRecalibrator - ReadGroupCovariate | |
| [2014-10-03 19:04] INFO 19:04:02,843 BaseRecalibrator - QualityScoreCovariate | |
| [2014-10-03 19:04] INFO 19:04:02,843 BaseRecalibrator - ContextCovariate | |
| [2014-10-03 19:04] INFO 19:04:02,844 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3 | |
| [2014-10-03 19:04] INFO 19:04:02,845 BaseRecalibrator - CycleCovariate | |
| [2014-10-03 19:04] INFO 19:04:02,847 ReadShardBalancer$1 - Loading BAM index data | |
| [2014-10-03 19:04] INFO 19:04:02,848 ReadShardBalancer$1 - Done loading BAM index data | |
| [2014-10-03 19:04] INFO 19:04:03,850 ReadShardBalancer$1 - Loading BAM index data | |
| [2014-10-03 19:04] INFO 19:04:03,852 ReadShardBalancer$1 - Done loading BAM index data | |
| [2014-10-03 19:04] INFO 19:04:08,351 BaseRecalibrator - Calculating quantized quality scores... | |
| [2014-10-03 19:04] INFO 19:04:08,404 BaseRecalibrator - Writing recalibration report... | |
| [2014-10-03 19:04] INFO 19:04:09,476 BaseRecalibrator - ...done! | |
| [2014-10-03 19:04] INFO 19:04:09,478 BaseRecalibrator - BaseRecalibrator was able to recalibrate 78308 reads | |
| [2014-10-03 19:04] INFO 19:04:09,479 ProgressMeter - done 78308.0 6.0 s 85.0 s 87.2% 6.0 s 0.0 s | |
| [2014-10-03 19:04] INFO 19:04:09,481 ProgressMeter - Total runtime 6.67 secs, 0.11 min, 0.00 hours | |
| [2014-10-03 19:04] INFO 19:04:09,481 MicroScheduler - 1258 reads were filtered out during the traversal out of approximately 79566 total reads (1.58%) | |
| [2014-10-03 19:04] INFO 19:04:09,482 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 19:04] INFO 19:04:09,487 MicroScheduler - -> 866 reads (1.09% of total) failing DuplicateReadFilter | |
| [2014-10-03 19:04] INFO 19:04:09,492 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter | |
| [2014-10-03 19:04] INFO 19:04:09,492 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 19:04] INFO 19:04:09,493 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter | |
| [2014-10-03 19:04] INFO 19:04:09,493 MicroScheduler - -> 392 reads (0.49% of total) failing MappingQualityZeroFilter | |
| [2014-10-03 19:04] INFO 19:04:09,494 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 19:04] INFO 19:04:09,495 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter | |
| [2014-10-03 19:04] INFO 19:04:16,042 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 19:04] multiprocessing: combine_sample_regions | |
| [2014-10-03 19:04] Identified 2 parallel analysis blocks | |
| Block sizes: | |
| min: 5000 | |
| 5%: 5479.75 | |
| 25%: 7398.75 | |
| median: 9797.5 | |
| 75%: 12196.25 | |
| 95%: 14115.25 | |
| 99%: 14499.05 | |
| max: 14595 | |
| Between block sizes: | |
| [] | |
| [2014-10-03 19:04] Timing: coverage | |
| [2014-10-03 19:04] Resource requests: freebayes, gatk, picard; memory: 2.0, 3.5, 3.5; cores: 1, 1, 1 | |
| [2014-10-03 19:04] Configuring 1 jobs to run, using 1 cores each with 3.8g of memory reserved for each job | |
| [2014-10-03 19:04] Timing: alignment post-processing | |
| [2014-10-03 19:04] multiprocessing: piped_bamprep | |
| [2014-10-03 19:04] GATK pre-alignment ('chrM', 0, 5000) : Test1 | |
| [2014-10-03 19:04] INFO 19:04:17,851 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:17,853 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53 | |
| [2014-10-03 19:04] INFO 19:04:17,853 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:04] INFO 19:04:17,854 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:04] INFO 19:04:17,856 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T PrintReads -L chrM:1-5000 -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.bam --downsample_to_coverage 10000 -BQSR /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.grp -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chrM/tx/tmpcATHGM/7_100326_FC6107FAAXX-sort-chrM_0_5000-prep-prealign.bam | |
| [2014-10-03 19:04] INFO 19:04:17,859 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:04] INFO 19:04:17,860 HelpFormatter - Date/Time: 2014/10/03 19:04:17 | |
| [2014-10-03 19:04] INFO 19:04:17,860 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:17,861 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:18,318 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:04] INFO 19:04:18,361 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000 | |
| [2014-10-03 19:04] INFO 19:04:18,367 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 19:04] INFO 19:04:18,375 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 19:04] INFO 19:04:18,383 IntervalUtils - Processing 5000 bp from intervals | |
| [2014-10-03 19:04] INFO 19:04:18,430 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 19:04] INFO 19:04:18,445 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:04] INFO 19:04:18,446 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:04] INFO 19:04:18,447 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 19:04] INFO 19:04:18,448 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime | |
| [2014-10-03 19:04] INFO 19:04:18,451 ReadShardBalancer$1 - Loading BAM index data | |
| [2014-10-03 19:04] INFO 19:04:18,452 ReadShardBalancer$1 - Done loading BAM index data | |
| [2014-10-03 19:04] INFO 19:04:20,893 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@74dee4ec | |
| [2014-10-03 19:04] INFO 19:04:20,897 ProgressMeter - done 79879.0 2.0 s 30.0 s 100.0% 2.0 s 0.0 s | |
| [2014-10-03 19:04] INFO 19:04:20,898 ProgressMeter - Total runtime 2.45 secs, 0.04 min, 0.00 hours | |
| [2014-10-03 19:04] INFO 19:04:20,900 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 79879 total reads (0.00%) | |
| [2014-10-03 19:04] INFO 19:04:20,901 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 19:04] INFO 19:04:20,902 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 19:04] INFO 19:04:20,902 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 19:04] Index BAM file: 7_100326_FC6107FAAXX-sort-chrM_0_5000-prep-prealign.bam | |
| [2014-10-03 19:04] GATK RealignerTargetCreator: 7_100326_FC6107FAAXX-sort-chrM_0_5000-prep-prealign.bam chrM:1-5000 | |
| [2014-10-03 19:04] GATK: RealignerTargetCreator | |
| [2014-10-03 19:04] INFO 19:04:22,776 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:22,779 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 19:04] INFO 19:04:22,779 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:04] INFO 19:04:22,780 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:04] INFO 19:04:22,783 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chrM/7_100326_FC6107FAAXX-sort-chrM_0_5000-prep-prealign.bam -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chrM/tx/tmp76Qo92/7_100326_FC6107FAAXX-sort-chrM_0_5000-prep-prealign-realign.intervals -l INFO -L chrM:1-5000 --interval_set_rule INTERSECTION --known /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment | |
| [2014-10-03 19:04] INFO 19:04:22,785 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:04] INFO 19:04:22,786 HelpFormatter - Date/Time: 2014/10/03 19:04:22 | |
| [2014-10-03 19:04] INFO 19:04:22,786 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:22,787 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:23,227 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:04] INFO 19:04:23,277 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:04] INFO 19:04:23,283 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 19:04] INFO 19:04:23,293 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 19:04] INFO 19:04:23,326 IntervalUtils - Processing 5000 bp from intervals | |
| [2014-10-03 19:04] WARN 19:04:23,328 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:04] INFO 19:04:23,375 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 19:04] INFO 19:04:23,390 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:04] INFO 19:04:23,391 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:04] INFO 19:04:23,392 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 19:04] INFO 19:04:23,393 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 19:04] INFO 19:04:25,415 ProgressMeter - done 5000.0 2.0 s 6.7 m 98.0% 2.0 s 0.0 s | |
| [2014-10-03 19:04] INFO 19:04:25,420 ProgressMeter - Total runtime 2.03 secs, 0.03 min, 0.00 hours | |
| [2014-10-03 19:04] INFO 19:04:25,420 MicroScheduler - 1274 reads were filtered out during the traversal out of approximately 79879 total reads (1.59%) | |
| [2014-10-03 19:04] INFO 19:04:25,421 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 19:04] INFO 19:04:25,422 MicroScheduler - -> 0 reads (0.00% of total) failing BadMateFilter | |
| [2014-10-03 19:04] INFO 19:04:25,423 MicroScheduler - -> 872 reads (1.09% of total) failing DuplicateReadFilter | |
| [2014-10-03 19:04] INFO 19:04:25,423 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter | |
| [2014-10-03 19:04] INFO 19:04:25,424 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 19:04] INFO 19:04:25,425 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter | |
| [2014-10-03 19:04] INFO 19:04:25,425 MicroScheduler - -> 402 reads (0.50% of total) failing MappingQualityZeroFilter | |
| [2014-10-03 19:04] INFO 19:04:25,426 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 19:04] INFO 19:04:25,427 MicroScheduler - -> 0 reads (0.00% of total) failing Platform454Filter | |
| [2014-10-03 19:04] INFO 19:04:25,428 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter | |
| [2014-10-03 19:04] INFO 19:04:31,675 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 19:04] GATK: realign ('chrM', 0, 5000) : Test1 | |
| [2014-10-03 19:04] INFO 19:04:33,420 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:33,422 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 19:04] INFO 19:04:33,423 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:04] INFO 19:04:33,423 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:04] INFO 19:04:33,426 HelpFormatter - Program Args: -T IndelRealigner -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chrM/7_100326_FC6107FAAXX-sort-chrM_0_5000-prep-prealign.bam -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -targetIntervals /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chrM/7_100326_FC6107FAAXX-sort-chrM_0_5000-prep-prealign-realign.intervals -L chrM:1-5000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chrM/tx/tmpBc4cpF/7_100326_FC6107FAAXX-sort-chrM_0_5000-prep.bam | |
| [2014-10-03 19:04] INFO 19:04:33,429 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:04] INFO 19:04:33,430 HelpFormatter - Date/Time: 2014/10/03 19:04:33 | |
| [2014-10-03 19:04] INFO 19:04:33,431 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:33,432 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:33,970 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:04] INFO 19:04:34,005 GenomeAnalysisEngine - Downsampling Settings: No downsampling | |
| [2014-10-03 19:04] INFO 19:04:34,010 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 19:04] INFO 19:04:34,019 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 19:04] INFO 19:04:34,027 IntervalUtils - Processing 5000 bp from intervals | |
| [2014-10-03 19:04] INFO 19:04:34,074 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 19:04] INFO 19:04:34,089 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:04] INFO 19:04:34,091 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:04] INFO 19:04:34,092 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 19:04] INFO 19:04:34,093 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime | |
| [2014-10-03 19:04] INFO 19:04:34,104 ReadShardBalancer$1 - Loading BAM index data | |
| [2014-10-03 19:04] INFO 19:04:34,105 ReadShardBalancer$1 - Done loading BAM index data | |
| [2014-10-03 19:04] INFO 19:04:38,659 ProgressMeter - done 79879.0 4.0 s 57.0 s 100.0% 4.0 s 0.0 s | |
| [2014-10-03 19:04] INFO 19:04:38,660 ProgressMeter - Total runtime 4.57 secs, 0.08 min, 0.00 hours | |
| [2014-10-03 19:04] INFO 19:04:38,662 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 79879 total reads (0.00%) | |
| [2014-10-03 19:04] INFO 19:04:38,663 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 19:04] INFO 19:04:38,664 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 19:04] INFO 19:04:38,665 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 19:04] INFO 19:04:44,933 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 19:04] Index BAM file: 7_100326_FC6107FAAXX-sort-chrM_0_5000-prep.bam | |
| [2014-10-03 19:04] GATK pre-alignment ('chr22', 0, 14595) : Test1 | |
| [2014-10-03 19:04] INFO 19:04:46,737 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:46,739 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53 | |
| [2014-10-03 19:04] INFO 19:04:46,739 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:04] INFO 19:04:46,740 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:04] INFO 19:04:46,743 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T PrintReads -L chr22:1-14595 -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.bam --downsample_to_coverage 10000 -BQSR /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.grp -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chr22/tx/tmpu9Q4ge/7_100326_FC6107FAAXX-sort-chr22_0_14595-prep-prealign.bam | |
| [2014-10-03 19:04] INFO 19:04:46,745 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:04] INFO 19:04:46,746 HelpFormatter - Date/Time: 2014/10/03 19:04:46 | |
| [2014-10-03 19:04] INFO 19:04:46,747 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:46,747 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:47,212 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:04] INFO 19:04:47,253 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000 | |
| [2014-10-03 19:04] INFO 19:04:47,259 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 19:04] INFO 19:04:47,268 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 19:04] INFO 19:04:47,275 IntervalUtils - Processing 14595 bp from intervals | |
| [2014-10-03 19:04] INFO 19:04:47,323 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 19:04] INFO 19:04:47,336 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:04] INFO 19:04:47,339 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:04] INFO 19:04:47,340 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 19:04] INFO 19:04:47,340 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime | |
| [2014-10-03 19:04] INFO 19:04:47,345 ReadShardBalancer$1 - Loading BAM index data | |
| [2014-10-03 19:04] INFO 19:04:47,346 ReadShardBalancer$1 - Done loading BAM index data | |
| [2014-10-03 19:04] INFO 19:04:47,392 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@74dee4ec | |
| [2014-10-03 19:04] INFO 19:04:47,397 ProgressMeter - done 104.0 0.0 s 9.2 m 99.3% 0.0 s 0.0 s | |
| [2014-10-03 19:04] INFO 19:04:47,398 ProgressMeter - Total runtime 0.06 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:04] INFO 19:04:47,400 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 104 total reads (0.00%) | |
| [2014-10-03 19:04] INFO 19:04:47,401 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 19:04] INFO 19:04:47,402 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 19:04] INFO 19:04:47,402 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 19:04] Index BAM file: 7_100326_FC6107FAAXX-sort-chr22_0_14595-prep-prealign.bam | |
| [2014-10-03 19:04] GATK RealignerTargetCreator: 7_100326_FC6107FAAXX-sort-chr22_0_14595-prep-prealign.bam chr22:1-14595 | |
| [2014-10-03 19:04] GATK: RealignerTargetCreator | |
| [2014-10-03 19:04] INFO 19:04:49,192 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:49,194 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 19:04] INFO 19:04:49,194 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:04] INFO 19:04:49,195 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:04] INFO 19:04:49,197 HelpFormatter - Program Args: -T RealignerTargetCreator -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chr22/7_100326_FC6107FAAXX-sort-chr22_0_14595-prep-prealign.bam -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chr22/tx/tmpCx6CTo/7_100326_FC6107FAAXX-sort-chr22_0_14595-prep-prealign-realign.intervals -l INFO -L chr22:1-14595 --interval_set_rule INTERSECTION --known /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment | |
| [2014-10-03 19:04] INFO 19:04:49,200 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:04] INFO 19:04:49,201 HelpFormatter - Date/Time: 2014/10/03 19:04:49 | |
| [2014-10-03 19:04] INFO 19:04:49,202 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:49,202 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:49,628 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:04] INFO 19:04:49,678 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:04] INFO 19:04:49,683 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 19:04] INFO 19:04:49,691 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 19:04] INFO 19:04:49,724 IntervalUtils - Processing 14595 bp from intervals | |
| [2014-10-03 19:04] WARN 19:04:49,728 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:04] INFO 19:04:49,775 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 19:04] INFO 19:04:49,791 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:04] INFO 19:04:49,791 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:04] INFO 19:04:49,792 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 19:04] INFO 19:04:49,793 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 19:04] INFO 19:04:50,354 ProgressMeter - done 14595.0 0.0 s 38.0 s 99.3% 0.0 s 0.0 s | |
| [2014-10-03 19:04] INFO 19:04:50,355 ProgressMeter - Total runtime 0.56 secs, 0.01 min, 0.00 hours | |
| [2014-10-03 19:04] INFO 19:04:50,358 MicroScheduler - 2 reads were filtered out during the traversal out of approximately 104 total reads (1.92%) | |
| [2014-10-03 19:04] INFO 19:04:50,367 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 19:04] INFO 19:04:50,368 MicroScheduler - -> 0 reads (0.00% of total) failing BadMateFilter | |
| [2014-10-03 19:04] INFO 19:04:50,369 MicroScheduler - -> 2 reads (1.92% of total) failing DuplicateReadFilter | |
| [2014-10-03 19:04] INFO 19:04:50,370 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter | |
| [2014-10-03 19:04] INFO 19:04:50,370 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 19:04] INFO 19:04:50,371 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter | |
| [2014-10-03 19:04] INFO 19:04:50,371 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityZeroFilter | |
| [2014-10-03 19:04] INFO 19:04:50,372 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 19:04] INFO 19:04:50,373 MicroScheduler - -> 0 reads (0.00% of total) failing Platform454Filter | |
| [2014-10-03 19:04] INFO 19:04:50,373 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter | |
| [2014-10-03 19:04] INFO 19:04:56,697 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 19:04] GATK: realign ('chr22', 0, 14595) : Test1 | |
| [2014-10-03 19:04] INFO 19:04:58,454 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:58,456 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 19:04] INFO 19:04:58,456 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:04] INFO 19:04:58,457 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:04] INFO 19:04:58,459 HelpFormatter - Program Args: -T IndelRealigner -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chr22/7_100326_FC6107FAAXX-sort-chr22_0_14595-prep-prealign.bam -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -targetIntervals /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chr22/7_100326_FC6107FAAXX-sort-chr22_0_14595-prep-prealign-realign.intervals -L chr22:1-14595 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chr22/tx/tmpXH7im2/7_100326_FC6107FAAXX-sort-chr22_0_14595-prep.bam | |
| [2014-10-03 19:04] INFO 19:04:58,462 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:04] INFO 19:04:58,462 HelpFormatter - Date/Time: 2014/10/03 19:04:58 | |
| [2014-10-03 19:04] INFO 19:04:58,463 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:58,463 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:04] INFO 19:04:59,000 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:04] INFO 19:04:59,035 GenomeAnalysisEngine - Downsampling Settings: No downsampling | |
| [2014-10-03 19:04] INFO 19:04:59,041 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 19:04] INFO 19:04:59,049 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 19:04] INFO 19:04:59,058 IntervalUtils - Processing 14595 bp from intervals | |
| [2014-10-03 19:04] INFO 19:04:59,105 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 19:04] INFO 19:04:59,121 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:04] INFO 19:04:59,122 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:04] INFO 19:04:59,123 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 19:04] INFO 19:04:59,124 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime | |
| [2014-10-03 19:04] INFO 19:04:59,134 ReadShardBalancer$1 - Loading BAM index data | |
| [2014-10-03 19:04] INFO 19:04:59,135 ReadShardBalancer$1 - Done loading BAM index data | |
| [2014-10-03 19:04] INFO 19:04:59,208 ProgressMeter - done 104.0 0.0 s 13.6 m 99.3% 0.0 s 0.0 s | |
| [2014-10-03 19:04] INFO 19:04:59,209 ProgressMeter - Total runtime 0.09 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:04] INFO 19:04:59,211 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 104 total reads (0.00%) | |
| [2014-10-03 19:04] INFO 19:04:59,212 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 19:04] INFO 19:04:59,212 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 19:04] INFO 19:04:59,213 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 19:05] INFO 19:05:05,552 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 19:05] Index BAM file: 7_100326_FC6107FAAXX-sort-chr22_0_14595-prep.bam | |
| [2014-10-03 19:05] Select unmapped reads | |
| [2014-10-03 19:05] Index BAM file: 7_100326_FC6107FAAXX-sort-nochrom-prep.bam | |
| [2014-10-03 19:05] Select unanalyzed reads | |
| [2014-10-03 19:05] Index BAM file: 7_100326_FC6107FAAXX-sort-noanalysis-prep.bam | |
| [2014-10-03 19:05] Timing: variant calling | |
| [2014-10-03 19:05] multiprocessing: variantcall_sample | |
| [2014-10-03 19:05] GATK: UnifiedGenotyper | |
| [2014-10-03 19:05] INFO 19:05:07,666 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:05] INFO 19:05:07,668 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 19:05] INFO 19:05:07,669 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:05] INFO 19:05:07,669 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:05] INFO 19:05:07,672 HelpFormatter - Program Args: -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --standard_min_confidence_threshold_for_calling 30.0 --standard_min_confidence_threshold_for_emitting 30.0 --downsample_to_coverage 2000 --downsampling_type BY_SAMPLE --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chrM/7_100326_FC6107FAAXX-sort-chrM_0_5000-prep.bam --dbsnp /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/chrM/TestBatch1-chrM_0_5000-raw-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/chrM/tx/tmpywLzQz/TestBatch1-chrM_0_5000-raw.vcf.gz -ploidy 1 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment | |
| [2014-10-03 19:05] INFO 19:05:07,675 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:05] INFO 19:05:07,676 HelpFormatter - Date/Time: 2014/10/03 19:05:07 | |
| [2014-10-03 19:05] INFO 19:05:07,676 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:05] INFO 19:05:07,677 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:05] INFO 19:05:08,261 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:05] INFO 19:05:08,327 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 2000 | |
| [2014-10-03 19:05] INFO 19:05:08,333 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 19:05] INFO 19:05:08,341 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 19:05] INFO 19:05:08,374 IntervalUtils - Processing 4900 bp from intervals | |
| [2014-10-03 19:05] WARN 19:05:08,377 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:05] INFO 19:05:08,424 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 19:05] INFO 19:05:08,438 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:05] INFO 19:05:08,439 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:05] INFO 19:05:08,439 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 19:05] INFO 19:05:08,440 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 19:05] INFO 19:05:08,997 AFCalcFactory - Requested ploidy 1 maxAltAlleles 6 not supported by requested model EXACT_INDEPENDENT looking for an option | |
| [2014-10-03 19:05] INFO 19:05:08,998 AFCalcFactory - Selecting model EXACT_GENERAL_PLOIDY | |
| [2014-10-03 19:05] INFO 19:05:13,827 ProgressMeter - done 4900.0 5.0 s 18.3 m 98.0% 5.0 s 0.0 s | |
| [2014-10-03 19:05] INFO 19:05:13,828 ProgressMeter - Total runtime 5.39 secs, 0.09 min, 0.00 hours | |
| [2014-10-03 19:05] INFO 19:05:13,829 MicroScheduler - 1258 reads were filtered out during the traversal out of approximately 79552 total reads (1.58%) | |
| [2014-10-03 19:05] INFO 19:05:13,830 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 19:05] INFO 19:05:13,830 MicroScheduler - -> 0 reads (0.00% of total) failing BadMateFilter | |
| [2014-10-03 19:05] INFO 19:05:13,831 MicroScheduler - -> 866 reads (1.09% of total) failing DuplicateReadFilter | |
| [2014-10-03 19:05] INFO 19:05:13,831 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter | |
| [2014-10-03 19:05] INFO 19:05:13,832 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 19:05] INFO 19:05:13,833 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter | |
| [2014-10-03 19:05] INFO 19:05:13,833 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 19:05] INFO 19:05:13,834 MicroScheduler - -> 392 reads (0.49% of total) failing UnmappedReadFilter | |
| [2014-10-03 19:05] INFO 19:05:20,206 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 19:05] GATK: UnifiedGenotyper | |
| [2014-10-03 19:05] INFO 19:05:22,049 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:05] INFO 19:05:22,052 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 19:05] INFO 19:05:22,052 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:05] INFO 19:05:22,053 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:05] INFO 19:05:22,055 HelpFormatter - Program Args: -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --standard_min_confidence_threshold_for_calling 30.0 --standard_min_confidence_threshold_for_emitting 30.0 --downsample_to_coverage 2000 --downsampling_type BY_SAMPLE --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chr22/7_100326_FC6107FAAXX-sort-chr22_0_14595-prep.bam --dbsnp /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/chr22/TestBatch1-chr22_0_14595-raw-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/chr22/tx/tmpfmBThi/TestBatch1-chr22_0_14595-raw.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment | |
| [2014-10-03 19:05] INFO 19:05:22,059 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:05] INFO 19:05:22,060 HelpFormatter - Date/Time: 2014/10/03 19:05:22 | |
| [2014-10-03 19:05] INFO 19:05:22,061 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:05] INFO 19:05:22,061 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:05] INFO 19:05:22,633 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:05] INFO 19:05:22,700 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 2000 | |
| [2014-10-03 19:05] INFO 19:05:22,706 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 19:05] INFO 19:05:22,718 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 19:05] INFO 19:05:22,750 IntervalUtils - Processing 345 bp from intervals | |
| [2014-10-03 19:05] WARN 19:05:22,752 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:05] INFO 19:05:22,798 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 19:05] INFO 19:05:22,812 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:05] INFO 19:05:22,815 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:05] INFO 19:05:22,816 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 19:05] INFO 19:05:22,816 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 19:05] INFO 19:05:23,069 ProgressMeter - done 345.0 0.0 s 12.3 m 87.0% 0.0 s 0.0 s | |
| [2014-10-03 19:05] INFO 19:05:23,070 ProgressMeter - Total runtime 0.26 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:05] INFO 19:05:23,071 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 14 total reads (0.00%) | |
| [2014-10-03 19:05] INFO 19:05:23,072 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 19:05] INFO 19:05:23,073 MicroScheduler - -> 0 reads (0.00% of total) failing BadMateFilter | |
| [2014-10-03 19:05] INFO 19:05:23,073 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter | |
| [2014-10-03 19:05] INFO 19:05:23,074 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter | |
| [2014-10-03 19:05] INFO 19:05:23,075 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 19:05] INFO 19:05:23,076 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter | |
| [2014-10-03 19:05] INFO 19:05:23,077 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 19:05] INFO 19:05:23,077 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter | |
| [2014-10-03 19:05] INFO 19:05:29,545 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 19:05] Genotyping with FreeBayes | |
| [2014-10-03 19:05] tabix index TestBatch1-chrM_0_5000-raw.vcf.gz | |
| [2014-10-03 19:05] GATK: VariantAnnotator | |
| [2014-10-03 19:05] INFO 19:05:33,532 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:05] INFO 19:05:33,535 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 19:05] INFO 19:05:33,536 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:05] INFO 19:05:33,537 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:05] INFO 19:05:33,540 HelpFormatter - Program Args: -T VariantAnnotator -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chrM/TestBatch1-chrM_0_5000-raw.vcf.gz --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chrM/tx/tmpxQSm7R/TestBatch1-chrM_0_5000-raw-gatkann.vcf.gz -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chrM/TestBatch1-chrM_0_5000-raw.vcf.gz --dbsnp /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chrM/7_100326_FC6107FAAXX-sort-chrM_0_5000-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality -A DepthPerAlleleBySample -A Coverage --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment | |
| [2014-10-03 19:05] INFO 19:05:33,543 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:05] INFO 19:05:33,543 HelpFormatter - Date/Time: 2014/10/03 19:05:33 | |
| [2014-10-03 19:05] INFO 19:05:33,544 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:05] INFO 19:05:33,545 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:05] INFO 19:05:34,057 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:05] INFO 19:05:34,125 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 | |
| [2014-10-03 19:05] INFO 19:05:34,130 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 19:05] INFO 19:05:34,140 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 19:05] INFO 19:05:34,198 IntervalUtils - Processing 9 bp from intervals | |
| [2014-10-03 19:05] WARN 19:05:34,200 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:05] WARN 19:05:34,201 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:05] INFO 19:05:34,273 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 19:05] INFO 19:05:34,288 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:05] INFO 19:05:34,289 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:05] INFO 19:05:34,290 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 19:05] INFO 19:05:34,291 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 19:05] INFO 19:05:35,637 VariantAnnotator - Processed 9 loci. | |
| [2014-10-03 19:05] | |
| [2014-10-03 19:05] INFO 19:05:35,646 ProgressMeter - done 45.0 1.0 s 8.4 h 88.9% 1.0 s 0.0 s | |
| [2014-10-03 19:05] INFO 19:05:35,647 ProgressMeter - Total runtime 1.36 secs, 0.02 min, 0.00 hours | |
| [2014-10-03 19:05] INFO 19:05:35,647 MicroScheduler - 45 reads were filtered out during the traversal out of approximately 6560 total reads (0.69%) | |
| [2014-10-03 19:05] INFO 19:05:35,648 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 19:05] INFO 19:05:35,649 MicroScheduler - -> 44 reads (0.67% of total) failing DuplicateReadFilter | |
| [2014-10-03 19:05] INFO 19:05:35,649 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter | |
| [2014-10-03 19:05] INFO 19:05:35,650 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 19:05] INFO 19:05:35,650 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 19:05] INFO 19:05:35,652 MicroScheduler - -> 1 reads (0.02% of total) failing UnmappedReadFilter | |
| [2014-10-03 19:05] INFO 19:05:41,967 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 19:05] Genotyping with FreeBayes | |
| [2014-10-03 19:05] tabix index TestBatch1-chr22_0_14595-raw.vcf.gz | |
| [2014-10-03 19:05] GATK: VariantAnnotator | |
| [2014-10-03 19:05] INFO 19:05:43,754 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:05] INFO 19:05:43,756 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 19:05] INFO 19:05:43,757 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:05] INFO 19:05:43,757 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:05] INFO 19:05:43,760 HelpFormatter - Program Args: -T VariantAnnotator -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chr22/TestBatch1-chr22_0_14595-raw.vcf.gz --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chr22/tx/tmpLnQTx3/TestBatch1-chr22_0_14595-raw-gatkann.vcf.gz -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chr22/TestBatch1-chr22_0_14595-raw.vcf.gz --dbsnp /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/bamprep/Test1/chr22/7_100326_FC6107FAAXX-sort-chr22_0_14595-prep.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality -A DepthPerAlleleBySample -A Coverage --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment | |
| [2014-10-03 19:05] INFO 19:05:43,762 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:05] INFO 19:05:43,763 HelpFormatter - Date/Time: 2014/10/03 19:05:43 | |
| [2014-10-03 19:05] INFO 19:05:43,764 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:05] INFO 19:05:43,764 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:05] INFO 19:05:44,251 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:05] INFO 19:05:44,312 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 | |
| [2014-10-03 19:05] INFO 19:05:44,319 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 19:05] INFO 19:05:44,327 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 19:05] INFO 19:05:44,382 IntervalUtils - Processing 3 bp from intervals | |
| [2014-10-03 19:05] WARN 19:05:44,384 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:05] WARN 19:05:44,391 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:05] INFO 19:05:44,456 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 19:05] INFO 19:05:44,474 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:05] INFO 19:05:44,475 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:05] INFO 19:05:44,476 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 19:05] INFO 19:05:44,477 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 19:05] INFO 19:05:44,660 VariantAnnotator - Processed 3 loci. | |
| [2014-10-03 19:05] | |
| [2014-10-03 19:05] INFO 19:05:44,668 ProgressMeter - done 6.0 0.0 s 8.9 h 66.7% 0.0 s 0.0 s | |
| [2014-10-03 19:05] INFO 19:05:44,670 ProgressMeter - Total runtime 0.19 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:05] INFO 19:05:44,670 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 9 total reads (0.00%) | |
| [2014-10-03 19:05] INFO 19:05:44,672 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 19:05] INFO 19:05:44,673 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter | |
| [2014-10-03 19:05] INFO 19:05:44,674 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter | |
| [2014-10-03 19:05] INFO 19:05:44,674 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 19:05] INFO 19:05:44,675 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 19:05] INFO 19:05:44,675 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter | |
| [2014-10-03 19:05] INFO 19:05:50,929 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 19:05] multiprocessing: concat_variant_files | |
| [2014-10-03 19:05] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:05] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:05] Concat variant files | |
| [2014-10-03 19:05] INFO 19:05:52,225 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 19:05] INFO 19:05:52,227 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants | |
| [2014-10-03 19:05] INFO 19:05:52,237 HelpFormatter - Program Args: -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -V /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/TestBatch1-files.list -out /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/tx/tmpmXUGZE/TestBatch1.vcf.gz -assumeSorted | |
| [2014-10-03 19:05] INFO 19:05:52,240 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:05] INFO 19:05:52,241 HelpFormatter - Date/Time: 2014/10/03 19:05:52 | |
| [2014-10-03 19:05] INFO 19:05:52,241 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 19:05] INFO 19:05:52,242 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 19:05] .. | |
| [2014-10-03 19:05] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:05] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:05] Concat variant files | |
| [2014-10-03 19:05] INFO 19:05:53,765 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 19:05] INFO 19:05:53,767 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants | |
| [2014-10-03 19:05] INFO 19:05:53,770 HelpFormatter - Program Args: -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -V /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/TestBatch1-files.list -out /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/tx/tmpv2zRE8/TestBatch1.vcf.gz -assumeSorted | |
| [2014-10-03 19:05] INFO 19:05:53,777 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:05] INFO 19:05:53,778 HelpFormatter - Date/Time: 2014/10/03 19:05:53 | |
| [2014-10-03 19:05] INFO 19:05:53,778 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 19:05] INFO 19:05:53,779 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 19:05] .. | |
| [2014-10-03 19:05] Resource requests: bamtools, bcbio_variation, fastqc, gatk, gemini, qsignature, samtools, snpeff; memory: 2.5, 3.5, 2.0, 2.0, 6.0; cores: 1, 1, 1, 1, 16, 1, 16, 1 | |
| [2014-10-03 19:05] Configuring 1 jobs to run, using 1 cores each with 6.2g of memory reserved for each job | |
| [2014-10-03 19:05] Timing: joint squaring off/backfilling | |
| [2014-10-03 19:05] Timing: variant post-processing | |
| [2014-10-03 19:05] multiprocessing: postprocess_variants | |
| [2014-10-03 19:05] Finalizing variant calls: Test1, gatk | |
| [2014-10-03 19:05] Calculating variation effects for Test1, gatk | |
| [2014-10-03 19:05] snpEff effects : Test1 | |
| [2014-10-03 19:05] | |
| [2014-10-03 19:05] WARNINGS: Some warning were detected | |
| [2014-10-03 19:05] Warning type Number of warnings | |
| [2014-10-03 19:05] WARNING_TRANSCRIPT_INCOMPLETE 19 | |
| [2014-10-03 19:05] WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS 9 | |
| [2014-10-03 19:05] | |
| [2014-10-03 19:05] | |
| [2014-10-03 19:05] tabix index TestBatch1-effects.vcf.gz | |
| [2014-10-03 19:05] Filtering for Test1, gatk | |
| [2014-10-03 19:05] bgzip TestBatch1-effects-ploidyfix.vcf | |
| [2014-10-03 19:05] tabix index TestBatch1-effects-ploidyfix.vcf.gz | |
| [2014-10-03 19:05] Subset to SNPs and indels | |
| [2014-10-03 19:05] tabix index TestBatch1-effects-ploidyfix-snp.vcf.gz | |
| [2014-10-03 19:05] Subset to SNPs and indels | |
| [2014-10-03 19:05] tabix index TestBatch1-effects-ploidyfix-indel.vcf.gz | |
| [2014-10-03 19:05] Hard filtering /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/TestBatch1-effects-ploidyfix-snp.vcf.gz with QD < 2.0 || MQ < 40.0 || FS > 60.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || HaplotypeScore > 13.0 : Test1 | |
| [2014-10-03 19:05] tabix index TestBatch1-effects-ploidyfix-snp-filterSNP.vcf.gz | |
| [2014-10-03 19:05] tabix index TestBatch1-effects-ploidyfix-indel-filterINDEL.vcf.gz | |
| [2014-10-03 19:05] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:05] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:05] Combine variant files | |
| [2014-10-03 19:05] INFO 19:05:56,976 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 19:05] INFO 19:05:56,978 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53 | |
| [2014-10-03 19:05] INFO 19:05:56,979 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:05] INFO 19:05:56,979 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:05] INFO 19:05:56,982 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/tx/tmpM_RbR7/TestBatch1-effects-ploidyfix-combined.vcf.gz --variant:v0 /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/TestBatch1-effects-ploidyfix-snp-filterSNP.vcf.gz --variant:v1 /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/TestBatch1-effects-ploidyfix-indel-filterINDEL.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-variantcall.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:05] INFO 19:05:56,985 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:05] INFO 19:05:56,985 HelpFormatter - Date/Time: 2014/10/03 19:05:56 | |
| [2014-10-03 19:05] INFO 19:05:56,986 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 19:05] INFO 19:05:56,987 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 19:05] INFO 19:05:57,460 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:05] INFO 19:05:57,507 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:05] INFO 19:05:57,552 IntervalUtils - Processing 5650 bp from intervals | |
| [2014-10-03 19:05] WARN 19:05:57,555 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:05] WARN 19:05:57,556 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:05] INFO 19:05:57,602 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:05] INFO 19:05:57,603 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:05] INFO 19:05:57,604 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:05] INFO 19:05:57,605 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 19:05] INFO 19:05:57,605 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 19:05] INFO 19:05:57,699 ProgressMeter - done 10.0 0.0 s 2.6 h 89.8% 0.0 s 0.0 s | |
| [2014-10-03 19:05] INFO 19:05:57,700 ProgressMeter - Total runtime 0.10 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:05] Remove stray NON_REF gVCF information from VCF output : Test1 | |
| [2014-10-03 19:05] tabix index TestBatch1-effects-ploidyfix-combined-gatkclean.vcf.gz | |
| [2014-10-03 19:05] Finalizing variant calls: Test1, freebayes | |
| [2014-10-03 19:05] Calculating variation effects for Test1, freebayes | |
| [2014-10-03 19:05] snpEff effects : Test1 | |
| [2014-10-03 19:05] | |
| [2014-10-03 19:05] WARNINGS: Some warning were detected | |
| [2014-10-03 19:05] Warning type Number of warnings | |
| [2014-10-03 19:05] WARNING_TRANSCRIPT_INCOMPLETE 19 | |
| [2014-10-03 19:05] WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS 9 | |
| [2014-10-03 19:05] | |
| [2014-10-03 19:05] | |
| [2014-10-03 19:05] tabix index TestBatch1-effects.vcf.gz | |
| [2014-10-03 19:05] Filtering for Test1, freebayes | |
| [2014-10-03 19:05] bgzip TestBatch1-effects-ploidyfix.vcf | |
| [2014-10-03 19:05] tabix index TestBatch1-effects-ploidyfix.vcf.gz | |
| [2014-10-03 19:05] Hard filtering /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/TestBatch1-effects-ploidyfix.vcf.gz with (AF[0] <= 0.5 && (DP < 4 || (DP < 13 && %QUAL < 10))) || (AF[0] > 0.5 && (DP < 4 && %QUAL < 50)) || (%QUAL < 458.0 && DP > 229 && AF[0] <= 0.5) : Test1 | |
| [2014-10-03 19:05] tabix index TestBatch1-effects-ploidyfix-filter.vcf.gz | |
| [2014-10-03 19:05] multiprocessing: split_variants_by_sample | |
| [2014-10-03 19:05] Timing: prepped BAM merging | |
| [2014-10-03 19:05] multiprocessing: delayed_bam_merge | |
| [2014-10-03 19:05] Merge bam files to 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:05] Index BAM file: 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:05] Timing: validation | |
| [2014-10-03 19:05] multiprocessing: compare_to_rm | |
| [2014-10-03 19:05] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:05] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:05] Comparing variant calls using bcbio.variation : Test1 | |
| [2014-10-03 19:06] 2014-10-03 19:06:02,785 [INFO ] MLog clients using log4j logging. | |
| [2014-10-03 19:06] 2014-10-03 19:06:03,072 [INFO ] State :begin :: {:desc "Starting variation analysis"} | |
| [2014-10-03 19:06] 2014-10-03 19:06:03,102 [INFO ] State :clean :: {:desc "Cleaning input VCF: ref"} | |
| [2014-10-03 19:06] 2014-10-03 19:06:03,325 [INFO ] State :merge :: {:desc "Merging multiple input files: ref"} | |
| [2014-10-03 19:06] 2014-10-03 19:06:03,327 [INFO ] State :prep :: {:desc "Prepare VCF, resorting to genome build: ref"} | |
| [2014-10-03 19:06] INFO 19:06:06,432 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:06,434 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:06,434 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:06,435 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:06,438 HelpFormatter - Program Args: -T SelectVariants --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-ref-prep.vcf --unsafe ALL --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/txtmp187614049633299100/Test1-ref-noref.vcf --excludeNonVariants --excludeFiltered -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:06,440 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:06,440 HelpFormatter - Date/Time: 2014/10/03 19:06:06 | |
| [2014-10-03 19:06] INFO 19:06:06,441 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:06,441 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:07,033 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:07,105 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:07,125 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:07,165 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:07,167 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:07,167 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:07,168 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:07,172 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:07,231 SelectVariants - 9 records processed. | |
| [2014-10-03 19:06] INFO 19:06:07,233 ProgressMeter - done 9.00e+00 0.0 s 2.0 h 1.0% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:07,234 ProgressMeter - Total runtime 0.07 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:07,320 NativeMethodAccessorImpl - State :normalize :: {:desc "Normalize MNP and indel variants: ref"} | |
| [2014-10-03 19:06] INFO 19:06:07,389 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:07,390 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:07,391 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:07,391 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:07,392 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/txtmp8064060563992750796/Test1-ref-noref-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-ref-noref.vcf | |
| [2014-10-03 19:06] INFO 19:06:07,392 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:07,393 HelpFormatter - Date/Time: 2014/10/03 19:06:07 | |
| [2014-10-03 19:06] INFO 19:06:07,393 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:07,394 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:07,400 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:07,424 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:07,432 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:07,433 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:07,434 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:07,435 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] 0 variants were aligned | |
| [2014-10-03 19:06] INFO 19:06:07,479 ProgressMeter - done 9.00e+00 0.0 s 83.6 m 0.4% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:07,483 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:07,653 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:07,663 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:07,663 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:07,664 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:07,664 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/txtmp8450124972544672212/Test1-ref-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-ref-worknomnp.vcf | |
| [2014-10-03 19:06] INFO 19:06:07,665 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:07,666 HelpFormatter - Date/Time: 2014/10/03 19:06:07 | |
| [2014-10-03 19:06] INFO 19:06:07,666 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:07,667 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:07,670 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:07,695 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:07,698 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:07,699 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:07,699 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:07,700 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] 0 variants were aligned | |
| [2014-10-03 19:06] INFO 19:06:07,716 ProgressMeter - done 9.00e+00 0.0 s 30.2 m 0.4% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:07,716 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:07,781 NativeMethodAccessorImpl - State :clean :: {:desc "Cleaning input VCF: eval"} | |
| [2014-10-03 19:06] INFO 19:06:07,782 NativeMethodAccessorImpl - State :merge :: {:desc "Merging multiple input files: eval"} | |
| [2014-10-03 19:06] INFO 19:06:07,783 NativeMethodAccessorImpl - State :prep :: {:desc "Prepare VCF, resorting to genome build: eval"} | |
| [2014-10-03 19:06] INFO 19:06:07,865 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:07,865 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:07,866 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:07,866 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:07,867 HelpFormatter - Program Args: -T SelectVariants --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/Test1-effects-ploidyfix-combined-gatkclean.vcf.gz --unsafe ALL --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/txtmp4303169743581826535/Test1-eval-noref.vcf --excludeNonVariants --excludeFiltered -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:07,867 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:07,868 HelpFormatter - Date/Time: 2014/10/03 19:06:07 | |
| [2014-10-03 19:06] INFO 19:06:07,869 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:07,869 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:07,889 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:07,910 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:07,913 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] WARN 19:06:07,914 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:06] INFO 19:06:07,915 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:07,916 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:07,916 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:07,917 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:07,917 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:07,963 SelectVariants - 10 records processed. | |
| [2014-10-03 19:06] INFO 19:06:07,964 ProgressMeter - done 1.00e+01 0.0 s 79.7 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:07,965 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:08,031 NativeMethodAccessorImpl - State :normalize :: {:desc "Normalize MNP and indel variants: eval"} | |
| [2014-10-03 19:06] INFO 19:06:08,067 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:08,067 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:08,068 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:08,068 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:08,069 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/txtmp3822763165043698892/Test1-eval-noref-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-eval-noref.vcf | |
| [2014-10-03 19:06] INFO 19:06:08,069 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:08,070 HelpFormatter - Date/Time: 2014/10/03 19:06:08 | |
| [2014-10-03 19:06] INFO 19:06:08,070 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:08,071 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:08,077 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:08,091 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:08,094 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:08,095 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:08,096 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:08,096 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] 0 variants were aligned | |
| [2014-10-03 19:06] INFO 19:06:08,135 ProgressMeter - done 9.00e+00 0.0 s 71.1 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:08,136 ProgressMeter - Total runtime 0.04 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:08,292 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:08,303 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:08,304 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:08,305 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:08,305 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/txtmp2439833142840402456/Test1-eval-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-eval-worknomnp.vcf | |
| [2014-10-03 19:06] INFO 19:06:08,306 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:08,307 HelpFormatter - Date/Time: 2014/10/03 19:06:08 | |
| [2014-10-03 19:06] INFO 19:06:08,307 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:08,308 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:08,311 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:08,347 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:08,360 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:08,361 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:08,362 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:08,362 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] 0 variants were aligned | |
| [2014-10-03 19:06] INFO 19:06:08,409 ProgressMeter - done 9.00e+00 0.0 s 87.3 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:08,410 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:08,491 NativeMethodAccessorImpl - State :combine :: {:desc "Creating merged VCF files for all comparisons"} | |
| [2014-10-03 19:06] INFO 19:06:08,494 NativeMethodAccessorImpl - State :annotate :: {:desc "Annotate VCFs with metrics"} | |
| [2014-10-03 19:06] INFO 19:06:08,495 NativeMethodAccessorImpl - State :filter :: {:desc "Post annotation filtering"} | |
| [2014-10-03 19:06] INFO 19:06:08,504 NativeMethodAccessorImpl - State :compare :: {:desc "Comparing VCFs: ref vs eval"} | |
| [2014-10-03 19:06] INFO 19:06:08,667 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:08,668 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:08,668 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:08,669 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:08,669 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-eval-nomnp-nosv.vcf --concordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-ref-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/txtmp414354238918790928/Test1-eval-ref-concordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:08,670 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:08,670 HelpFormatter - Date/Time: 2014/10/03 19:06:08 | |
| [2014-10-03 19:06] INFO 19:06:08,671 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:08,671 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:08,681 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:08,693 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:08,705 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:08,706 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:08,707 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:08,708 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:08,708 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:08,709 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:08,713 SelectVariants - Selecting only variants concordant with the track: concordance | |
| [2014-10-03 19:06] INFO 19:06:08,747 SelectVariants - 9 records processed. | |
| [2014-10-03 19:06] INFO 19:06:08,753 ProgressMeter - done 1.00e+01 0.0 s 74.4 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:08,753 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:08,875 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:08,876 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:08,876 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:08,877 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:08,878 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-ref-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-eval-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/txtmp6119775709524485127/Test1-ref-eval-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:08,878 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:08,879 HelpFormatter - Date/Time: 2014/10/03 19:06:08 | |
| [2014-10-03 19:06] INFO 19:06:08,879 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:08,880 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:08,889 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:08,901 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:08,909 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:08,910 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:08,911 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:08,911 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:08,912 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:08,913 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:08,914 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:06] INFO 19:06:08,932 SelectVariants - 9 records processed. | |
| [2014-10-03 19:06] INFO 19:06:08,933 ProgressMeter - done 1.00e+01 0.0 s 36.1 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:08,934 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:09,033 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:09,033 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:09,034 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:09,035 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:09,036 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-eval-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/prep/Test1-ref-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/txtmp1064424960648047326/Test1-eval-ref-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:09,036 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:09,037 HelpFormatter - Date/Time: 2014/10/03 19:06:09 | |
| [2014-10-03 19:06] INFO 19:06:09,037 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:09,038 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:09,044 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:09,056 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:09,064 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:09,065 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:09,066 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:09,066 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:09,067 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:09,068 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:09,068 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:06] INFO 19:06:09,085 SelectVariants - 9 records processed. | |
| [2014-10-03 19:06] INFO 19:06:09,087 ProgressMeter - done 1.00e+01 0.0 s 34.4 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:09,088 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:09,225 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:09,226 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:09,227 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:09,227 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:09,228 HelpFormatter - Program Args: -T VariantAnnotator --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.bam --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/Test1-ref-eval-discordance-asref.vcf --allow_potentially_misencoded_quality_scores -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/txtmp6687571908364826829/Test1-ref-eval-discordance-asref-annotated.vcf -A DepthOfCoverage -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/Test1-ref-eval-discordance-asref.vcf | |
| [2014-10-03 19:06] INFO 19:06:09,228 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:09,229 HelpFormatter - Date/Time: 2014/10/03 19:06:09 | |
| [2014-10-03 19:06] INFO 19:06:09,229 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:09,230 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:09,248 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:09,278 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 | |
| [2014-10-03 19:06] INFO 19:06:09,287 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 19:06] INFO 19:06:09,288 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.00 | |
| [2014-10-03 19:06] INFO 19:06:09,292 IntervalUtils - Processing 1 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:09,293 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 19:06] INFO 19:06:09,319 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:09,320 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:09,320 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:09,615 VariantAnnotator - Processed 1 loci. | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] INFO 19:06:09,627 ProgressMeter - done 1.00e+00 0.0 s 85.3 h 0.0% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:09,628 ProgressMeter - Total runtime 0.31 secs, 0.01 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:09,629 MicroScheduler - 12 reads were filtered out during the traversal out of approximately 1152 total reads (1.04%) | |
| [2014-10-03 19:06] INFO 19:06:09,630 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 19:06] INFO 19:06:09,630 MicroScheduler - -> 11 reads (0.95% of total) failing DuplicateReadFilter | |
| [2014-10-03 19:06] INFO 19:06:09,631 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter | |
| [2014-10-03 19:06] INFO 19:06:09,631 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 19:06] INFO 19:06:09,632 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 19:06] INFO 19:06:09,632 MicroScheduler - -> 1 reads (0.09% of total) failing UnmappedReadFilter | |
| [2014-10-03 19:06] INFO 19:06:09,738 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:09,739 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:09,740 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:09,740 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:09,741 HelpFormatter - Program Args: -T CombineVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/txtmp7752543104617281248/Test1-eval-ref-discordance-fullcombine.vcf --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null --variant:v0 /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/Test1-eval-ref-discordance.vcf --variant:v1 /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/Test1-ref-eval-discordance-asref-annotated.vcf --genotypemergeoption PRIORITIZE | |
| [2014-10-03 19:06] INFO 19:06:09,741 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:09,742 HelpFormatter - Date/Time: 2014/10/03 19:06:09 | |
| [2014-10-03 19:06] INFO 19:06:09,742 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:09,743 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:09,748 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:09,760 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:09,769 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:09,769 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:09,770 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:09,770 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:09,792 ProgressMeter - done 2.00e+00 0.0 s 3.1 h 84.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:09,795 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:09,918 NativeMethodAccessorImpl - State :summary :: {:desc "Summarize comparisons"} | |
| [2014-10-03 19:06] INFO 19:06:11,174 C3P0Registry - Initializing c3p0-0.9.1.2 [built 21-May-2007 15:04:56; debug? true; trace: 10] | |
| [2014-10-03 19:06] INFO 19:06:11,243 AbstractPoolBackedDataSource - Initializing c3p0 pool... com.mchange.v2.c3p0.ComboPooledDataSource [ acquireIncrement -> 3, acquireRetryAttempts -> 30, acquireRetryDelay -> 1000, autoCommitOnClose -> false, automaticTestTable -> null, breakAfterAcquireFailure -> false, checkoutTimeout -> 0, connectionCustomizerClassName -> null, connectionTesterClassName -> com.mchange.v2.c3p0.impl.DefaultConnectionTester, dataSourceName -> 2rvy8f941nrmdlp1qxwmd|6208176a, debugUnreturnedConnectionStackTraces -> false, description -> null, driverClass -> org.sqlite.JDBC, factoryClassLocation -> null, forceIgnoreUnresolvedTransactions -> false, identityToken -> 2rvy8f941nrmdlp1qxwmd|6208176a, idleConnectionTestPeriod -> 0, initialPoolSize -> 3, jdbcUrl -> jdbc:sqlite:/home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk/work/Test1-eval-ref-discordance-annotate-gemini.db, maxAdministrativeTaskTime -> 0, maxConnectionAge -> 0, maxIdleTime -> 0, maxIdleTimeExcessConnections -> 0, maxPoolSize -> 15, maxStatements -> 0, maxStatementsPerConnection -> 0, minPoolSize -> 3, numHelperThreads -> 3, numThreadsAwaitingCheckoutDefaultUser -> 0, preferredTestQuery -> null, properties -> {}, propertyCycle -> 0, testConnectionOnCheckin -> false, testConnectionOnCheckout -> false, unreturnedConnectionTimeout -> 0, usesTraditionalReflectiveProxies -> false ] | |
| [2014-10-03 19:06] INFO 19:06:11,486 NativeMethodAccessorImpl - State :finished :: {:desc "Finished"} | |
| [2014-10-03 19:06] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:06] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:06] Comparing variant calls using bcbio.variation : Test1 | |
| [2014-10-03 19:06] 2014-10-03 19:06:14,209 [INFO ] MLog clients using log4j logging. | |
| [2014-10-03 19:06] 2014-10-03 19:06:14,455 [INFO ] State :begin :: {:desc "Starting variation analysis"} | |
| [2014-10-03 19:06] 2014-10-03 19:06:14,483 [INFO ] State :clean :: {:desc "Cleaning input VCF: ref"} | |
| [2014-10-03 19:06] 2014-10-03 19:06:14,683 [INFO ] State :merge :: {:desc "Merging multiple input files: ref"} | |
| [2014-10-03 19:06] 2014-10-03 19:06:14,684 [INFO ] State :prep :: {:desc "Prepare VCF, resorting to genome build: ref"} | |
| [2014-10-03 19:06] INFO 19:06:17,617 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:17,619 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:17,620 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:17,620 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:17,624 HelpFormatter - Program Args: -T SelectVariants --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-ref-prep.vcf --unsafe ALL --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/txtmp3121284386177337517/Test1-ref-noref.vcf --excludeNonVariants --excludeFiltered -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:17,627 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:17,627 HelpFormatter - Date/Time: 2014/10/03 19:06:17 | |
| [2014-10-03 19:06] INFO 19:06:17,628 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:17,628 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:18,199 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:18,269 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:18,286 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:18,324 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:18,325 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:18,326 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:18,327 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:18,331 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:18,398 SelectVariants - 9 records processed. | |
| [2014-10-03 19:06] INFO 19:06:18,400 ProgressMeter - done 9.00e+00 0.0 s 2.3 h 1.0% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:18,401 ProgressMeter - Total runtime 0.07 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:18,487 NativeMethodAccessorImpl - State :normalize :: {:desc "Normalize MNP and indel variants: ref"} | |
| [2014-10-03 19:06] INFO 19:06:18,549 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:18,550 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:18,551 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:18,551 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:18,552 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/txtmp8096583205080670922/Test1-ref-noref-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-ref-noref.vcf | |
| [2014-10-03 19:06] INFO 19:06:18,552 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:18,553 HelpFormatter - Date/Time: 2014/10/03 19:06:18 | |
| [2014-10-03 19:06] INFO 19:06:18,553 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:18,554 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:18,558 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:18,579 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:18,587 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:18,588 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:18,591 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:18,591 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] 0 variants were aligned | |
| [2014-10-03 19:06] INFO 19:06:18,637 ProgressMeter - done 9.00e+00 0.0 s 84.8 m 0.4% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:18,642 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:18,801 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:18,811 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:18,811 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:18,812 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:18,812 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/txtmp8738950949746620985/Test1-ref-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-ref-worknomnp.vcf | |
| [2014-10-03 19:06] INFO 19:06:18,813 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:18,813 HelpFormatter - Date/Time: 2014/10/03 19:06:18 | |
| [2014-10-03 19:06] INFO 19:06:18,815 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:18,815 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:18,821 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:18,850 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:18,853 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:18,854 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:18,854 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:18,854 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] 0 variants were aligned | |
| [2014-10-03 19:06] INFO 19:06:18,873 ProgressMeter - done 9.00e+00 0.0 s 33.9 m 0.4% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:18,873 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:18,935 NativeMethodAccessorImpl - State :clean :: {:desc "Cleaning input VCF: eval"} | |
| [2014-10-03 19:06] INFO 19:06:18,937 NativeMethodAccessorImpl - State :merge :: {:desc "Merging multiple input files: eval"} | |
| [2014-10-03 19:06] INFO 19:06:18,937 NativeMethodAccessorImpl - State :prep :: {:desc "Prepare VCF, resorting to genome build: eval"} | |
| [2014-10-03 19:06] INFO 19:06:19,018 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:19,022 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:19,023 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:19,024 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:19,024 HelpFormatter - Program Args: -T SelectVariants --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/Test1-effects-ploidyfix-filter.vcf.gz --unsafe ALL --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/txtmp7094813969938228658/Test1-eval-noref.vcf --excludeNonVariants --excludeFiltered -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:19,025 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:19,025 HelpFormatter - Date/Time: 2014/10/03 19:06:19 | |
| [2014-10-03 19:06] INFO 19:06:19,026 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:19,027 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:19,042 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:19,061 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:19,064 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] WARN 19:06:19,065 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:06] INFO 19:06:19,066 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:19,067 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:19,067 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:19,067 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:19,068 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:19,138 SelectVariants - 11 records processed. | |
| [2014-10-03 19:06] INFO 19:06:19,145 ProgressMeter - done 1.10e+01 0.0 s 118.3 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:19,146 ProgressMeter - Total runtime 0.08 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:19,237 NativeMethodAccessorImpl - State :normalize :: {:desc "Normalize MNP and indel variants: eval"} | |
| [2014-10-03 19:06] INFO 19:06:19,268 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:19,268 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:19,269 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:19,270 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:19,270 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/txtmp4534449161602788745/Test1-eval-noref-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-eval-noref.vcf | |
| [2014-10-03 19:06] INFO 19:06:19,271 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:19,271 HelpFormatter - Date/Time: 2014/10/03 19:06:19 | |
| [2014-10-03 19:06] INFO 19:06:19,272 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:19,272 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:19,277 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:19,289 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:19,293 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:19,294 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:19,294 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:19,296 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] 0 variants were aligned | |
| [2014-10-03 19:06] INFO 19:06:19,318 ProgressMeter - done 1.10e+01 0.0 s 35.3 m 84.4% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:19,318 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:19,464 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:19,467 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:19,468 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:19,468 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:19,469 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/txtmp1194373520598623920/Test1-eval-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-eval-worknomnp.vcf | |
| [2014-10-03 19:06] INFO 19:06:19,469 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:19,470 HelpFormatter - Date/Time: 2014/10/03 19:06:19 | |
| [2014-10-03 19:06] INFO 19:06:19,470 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:19,471 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:19,476 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:19,519 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:19,523 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:19,523 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:19,524 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:19,525 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] 0 variants were aligned | |
| [2014-10-03 19:06] INFO 19:06:19,555 ProgressMeter - done 1.10e+01 0.0 s 46.5 m 84.4% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:19,556 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:19,630 NativeMethodAccessorImpl - State :combine :: {:desc "Creating merged VCF files for all comparisons"} | |
| [2014-10-03 19:06] INFO 19:06:19,632 NativeMethodAccessorImpl - State :annotate :: {:desc "Annotate VCFs with metrics"} | |
| [2014-10-03 19:06] INFO 19:06:19,633 NativeMethodAccessorImpl - State :filter :: {:desc "Post annotation filtering"} | |
| [2014-10-03 19:06] INFO 19:06:19,643 NativeMethodAccessorImpl - State :compare :: {:desc "Comparing VCFs: ref vs eval"} | |
| [2014-10-03 19:06] INFO 19:06:19,866 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:19,867 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:19,867 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:19,868 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:19,868 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-eval-nomnp-nosv.vcf --concordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-ref-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/txtmp4167094807114282414/Test1-eval-ref-concordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:19,874 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:19,875 HelpFormatter - Date/Time: 2014/10/03 19:06:19 | |
| [2014-10-03 19:06] INFO 19:06:19,876 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:19,876 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:19,889 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:19,901 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:19,913 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:19,914 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:19,915 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:19,915 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:19,916 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:19,917 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:19,918 SelectVariants - Selecting only variants concordant with the track: concordance | |
| [2014-10-03 19:06] INFO 19:06:19,957 SelectVariants - 11 records processed. | |
| [2014-10-03 19:06] INFO 19:06:19,958 ProgressMeter - done 1.10e+01 0.0 s 64.9 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:19,960 ProgressMeter - Total runtime 0.04 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:20,072 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:20,076 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:20,077 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:20,078 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:20,078 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-ref-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-eval-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/txtmp4312749355378362827/Test1-ref-eval-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:20,079 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:20,079 HelpFormatter - Date/Time: 2014/10/03 19:06:20 | |
| [2014-10-03 19:06] INFO 19:06:20,080 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:20,080 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:20,087 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:20,099 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:20,105 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:20,107 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:20,107 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:20,107 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:20,108 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:20,108 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:20,110 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:06] INFO 19:06:20,125 SelectVariants - 9 records processed. | |
| [2014-10-03 19:06] INFO 19:06:20,127 ProgressMeter - done 1.10e+01 0.0 s 29.5 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:20,128 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:20,213 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:20,213 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:20,214 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:20,214 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:20,215 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-eval-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-ref-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/txtmp7610814574558559290/Test1-eval-ref-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:20,216 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:20,216 HelpFormatter - Date/Time: 2014/10/03 19:06:20 | |
| [2014-10-03 19:06] INFO 19:06:20,217 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:20,217 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:20,227 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:20,248 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:20,268 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:20,269 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:20,269 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:20,270 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:20,270 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:20,275 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:20,277 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:06] INFO 19:06:20,302 SelectVariants - 11 records processed. | |
| [2014-10-03 19:06] INFO 19:06:20,311 ProgressMeter - done 1.10e+01 0.0 s 62.3 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:20,312 ProgressMeter - Total runtime 0.04 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:20,425 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:20,430 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:20,431 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:20,431 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:20,432 HelpFormatter - Program Args: -T VariantAnnotator --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.bam --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/Test1-ref-eval-discordance-asref.vcf --allow_potentially_misencoded_quality_scores -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/txtmp3948113297250161272/Test1-ref-eval-discordance-asref-annotated.vcf -A DepthOfCoverage -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/Test1-ref-eval-discordance-asref.vcf | |
| [2014-10-03 19:06] INFO 19:06:20,433 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:20,433 HelpFormatter - Date/Time: 2014/10/03 19:06:20 | |
| [2014-10-03 19:06] INFO 19:06:20,434 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:20,434 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:20,442 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:20,462 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 | |
| [2014-10-03 19:06] INFO 19:06:20,463 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 19:06] INFO 19:06:20,465 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.00 | |
| [2014-10-03 19:06] WARN 19:06:20,470 IntervalUtils - The interval file /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/Test1-ref-eval-discordance-asref.vcf contains no intervals that could be parsed. | |
| [2014-10-03 19:06] INFO 19:06:20,470 IntervalUtils - Processing 0 bp from intervals | |
| [2014-10-03 19:06] WARN 19:06:20,471 GenomeAnalysisEngine - The given combination of -L and -XL options results in an empty set. No intervals to process. | |
| [2014-10-03 19:06] INFO 19:06:20,472 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 19:06] INFO 19:06:20,473 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:20,474 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:20,474 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:20,490 VariantAnnotator - Processed 0 loci. | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] INFO 19:06:20,494 ProgressMeter - done 0.00e+00 0.0 s 5.1 h 0.0% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:20,495 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:20,588 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:20,589 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:20,589 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:20,590 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:20,591 HelpFormatter - Program Args: -T CombineVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/txtmp2152950564747554792/Test1-eval-ref-discordance-fullcombine.vcf --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null --variant:v0 /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/Test1-eval-ref-discordance.vcf --variant:v1 /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/Test1-ref-eval-discordance-asref-annotated.vcf --genotypemergeoption PRIORITIZE | |
| [2014-10-03 19:06] INFO 19:06:20,592 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:20,592 HelpFormatter - Date/Time: 2014/10/03 19:06:20 | |
| [2014-10-03 19:06] INFO 19:06:20,593 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:20,593 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:20,600 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:20,611 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:20,618 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:20,619 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:20,619 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:20,620 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:20,632 ProgressMeter - done 2.00e+00 0.0 s 99.3 m 84.4% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:20,632 ProgressMeter - Total runtime 0.01 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:20,723 NativeMethodAccessorImpl - State :summary :: {:desc "Summarize comparisons"} | |
| [2014-10-03 19:06] INFO 19:06:21,684 C3P0Registry - Initializing c3p0-0.9.1.2 [built 21-May-2007 15:04:56; debug? true; trace: 10] | |
| [2014-10-03 19:06] INFO 19:06:21,750 AbstractPoolBackedDataSource - Initializing c3p0 pool... com.mchange.v2.c3p0.ComboPooledDataSource [ acquireIncrement -> 3, acquireRetryAttempts -> 30, acquireRetryDelay -> 1000, autoCommitOnClose -> false, automaticTestTable -> null, breakAfterAcquireFailure -> false, checkoutTimeout -> 0, connectionCustomizerClassName -> null, connectionTesterClassName -> com.mchange.v2.c3p0.impl.DefaultConnectionTester, dataSourceName -> 2rvy8f941nrmlps1joav9o|5e3d54d4, debugUnreturnedConnectionStackTraces -> false, description -> null, driverClass -> org.sqlite.JDBC, factoryClassLocation -> null, forceIgnoreUnresolvedTransactions -> false, identityToken -> 2rvy8f941nrmlps1joav9o|5e3d54d4, idleConnectionTestPeriod -> 0, initialPoolSize -> 3, jdbcUrl -> jdbc:sqlite:/home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/Test1-eval-ref-discordance-annotate-gemini.db, maxAdministrativeTaskTime -> 0, maxConnectionAge -> 0, maxIdleTime -> 0, maxIdleTimeExcessConnections -> 0, maxPoolSize -> 15, maxStatements -> 0, maxStatementsPerConnection -> 0, minPoolSize -> 3, numHelperThreads -> 3, numThreadsAwaitingCheckoutDefaultUser -> 0, preferredTestQuery -> null, properties -> {}, propertyCycle -> 0, testConnectionOnCheckin -> false, testConnectionOnCheckout -> false, unreturnedConnectionTimeout -> 0, usesTraditionalReflectiveProxies -> false ] | |
| [2014-10-03 19:06] INFO 19:06:22,100 NativeMethodAccessorImpl - State :finished :: {:desc "Finished"} | |
| [2014-10-03 19:06] Timing: ensemble calling | |
| [2014-10-03 19:06] multiprocessing: combine_calls | |
| [2014-10-03 19:06] Ensemble consensus calls for TestBatch1: gatk,freebayes | |
| [2014-10-03 19:06] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:06] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:06] Ensemble calling: TestBatch1 | |
| [2014-10-03 19:06] 2014-10-03 19:06:24,876 [INFO ] MLog clients using log4j logging. | |
| [2014-10-03 19:06] 2014-10-03 19:06:25,419 [INFO ] State :begin :: {:desc "Starting variation analysis"} | |
| [2014-10-03 19:06] 2014-10-03 19:06:25,479 [INFO ] State :clean :: {:desc "Cleaning input VCF: combo"} | |
| [2014-10-03 19:06] 2014-10-03 19:06:25,481 [INFO ] State :merge :: {:desc "Merging multiple input files: combo"} | |
| [2014-10-03 19:06] 2014-10-03 19:06:25,481 [INFO ] State :prep :: {:desc "Prepare VCF, resorting to genome build: combo"} | |
| [2014-10-03 19:06] 2014-10-03 19:06:25,501 [INFO ] State :normalize :: {:desc "Normalize MNP and indel variants: combo"} | |
| [2014-10-03 19:06] INFO 19:06:27,936 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:27,938 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:27,939 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:27,939 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:27,942 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/txtmp4498463718846189278/Test1-effects-ploidyfix-combined-gatkclean-leftalign.vcf.gz --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/Test1-effects-ploidyfix-combined-gatkclean.vcf.gz | |
| [2014-10-03 19:06] INFO 19:06:27,944 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:27,945 HelpFormatter - Date/Time: 2014/10/03 19:06:27 | |
| [2014-10-03 19:06] INFO 19:06:27,945 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:27,947 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:28,546 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:28,616 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] WARN 19:06:28,627 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:06] INFO 19:06:28,668 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:28,669 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:28,669 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:28,670 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] 0 variants were aligned | |
| [2014-10-03 19:06] INFO 19:06:28,760 ProgressMeter - done 1.00e+01 0.0 s 2.5 h 84.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:28,761 ProgressMeter - Total runtime 0.09 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:28,963 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:28,964 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:28,965 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:28,965 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:28,966 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/txtmp4812700798295934928/Test1-combo-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-worknomnp.vcf | |
| [2014-10-03 19:06] INFO 19:06:28,967 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:28,967 HelpFormatter - Date/Time: 2014/10/03 19:06:28 | |
| [2014-10-03 19:06] INFO 19:06:28,968 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:28,968 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:28,979 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:29,000 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:29,016 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:29,019 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:29,020 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:29,021 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] 0 variants were aligned | |
| [2014-10-03 19:06] INFO 19:06:29,065 ProgressMeter - done 1.00e+01 0.0 s 74.7 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:29,066 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:29,162 NativeMethodAccessorImpl - State :clean :: {:desc "Cleaning input VCF: gatk"} | |
| [2014-10-03 19:06] INFO 19:06:29,167 NativeMethodAccessorImpl - State :merge :: {:desc "Merging multiple input files: gatk"} | |
| [2014-10-03 19:06] INFO 19:06:29,168 NativeMethodAccessorImpl - State :prep :: {:desc "Prepare VCF, resorting to genome build: gatk"} | |
| [2014-10-03 19:06] INFO 19:06:29,180 NativeMethodAccessorImpl - State :normalize :: {:desc "Normalize MNP and indel variants: gatk"} | |
| [2014-10-03 19:06] INFO 19:06:29,257 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:29,266 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:29,267 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:29,267 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:29,268 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/txtmp2607744883880813754/Test1-effects-ploidyfix-combined-gatkclean-leftalign.vcf.gz --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/gatk/Test1-effects-ploidyfix-combined-gatkclean.vcf.gz | |
| [2014-10-03 19:06] INFO 19:06:29,269 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:29,269 HelpFormatter - Date/Time: 2014/10/03 19:06:29 | |
| [2014-10-03 19:06] INFO 19:06:29,270 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:29,270 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:29,274 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:29,304 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] WARN 19:06:29,311 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:06] INFO 19:06:29,316 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:29,317 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:29,317 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:29,318 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] 0 variants were aligned | |
| [2014-10-03 19:06] INFO 19:06:29,336 ProgressMeter - done 1.00e+01 0.0 s 31.2 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:29,337 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:29,481 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:29,482 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:29,483 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:29,483 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:29,484 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/txtmp2282734969209565752/Test1-gatk-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-worknomnp.vcf | |
| [2014-10-03 19:06] INFO 19:06:29,484 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:29,485 HelpFormatter - Date/Time: 2014/10/03 19:06:29 | |
| [2014-10-03 19:06] INFO 19:06:29,485 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:29,486 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:29,490 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:29,502 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:29,506 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:29,507 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:29,507 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:29,508 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] 0 variants were aligned | |
| [2014-10-03 19:06] INFO 19:06:29,527 ProgressMeter - done 1.00e+01 0.0 s 31.8 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:29,527 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:29,600 NativeMethodAccessorImpl - State :clean :: {:desc "Cleaning input VCF: freebayes"} | |
| [2014-10-03 19:06] INFO 19:06:29,601 NativeMethodAccessorImpl - State :merge :: {:desc "Merging multiple input files: freebayes"} | |
| [2014-10-03 19:06] INFO 19:06:29,602 NativeMethodAccessorImpl - State :prep :: {:desc "Prepare VCF, resorting to genome build: freebayes"} | |
| [2014-10-03 19:06] INFO 19:06:29,607 NativeMethodAccessorImpl - State :normalize :: {:desc "Normalize MNP and indel variants: freebayes"} | |
| [2014-10-03 19:06] INFO 19:06:29,656 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:29,657 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:29,657 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:29,659 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:29,660 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/txtmp8551825068139564155/Test1-effects-ploidyfix-filter-leftalign.vcf.gz --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/Test1-effects-ploidyfix-filter.vcf.gz | |
| [2014-10-03 19:06] INFO 19:06:29,660 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:29,661 HelpFormatter - Date/Time: 2014/10/03 19:06:29 | |
| [2014-10-03 19:06] INFO 19:06:29,662 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:29,662 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:29,666 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:29,695 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] WARN 19:06:29,698 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:06] INFO 19:06:29,698 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:29,699 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:29,699 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:29,703 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] 0 variants were aligned | |
| [2014-10-03 19:06] INFO 19:06:29,731 ProgressMeter - done 1.20e+01 0.0 s 43.6 m 84.4% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:29,732 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:29,933 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:29,942 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:29,943 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:29,944 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:29,944 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/txtmp3035816656344932018/Test1-freebayes-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-freebayes-worknomnp.vcf | |
| [2014-10-03 19:06] INFO 19:06:29,945 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:29,945 HelpFormatter - Date/Time: 2014/10/03 19:06:29 | |
| [2014-10-03 19:06] INFO 19:06:29,946 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:29,946 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:29,950 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:29,995 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:30,000 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:30,001 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:30,001 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:30,002 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] 0 variants were aligned | |
| [2014-10-03 19:06] INFO 19:06:30,052 ProgressMeter - done 1.20e+01 0.0 s 69.8 m 84.4% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:30,055 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:30,137 NativeMethodAccessorImpl - State :combine :: {:desc "Creating merged VCF files for all comparisons"} | |
| [2014-10-03 19:06] INFO 19:06:30,139 NativeMethodAccessorImpl - State :annotate :: {:desc "Annotate VCFs with metrics"} | |
| [2014-10-03 19:06] INFO 19:06:30,140 NativeMethodAccessorImpl - State :filter :: {:desc "Post annotation filtering"} | |
| [2014-10-03 19:06] INFO 19:06:30,219 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:30,222 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:30,223 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:30,224 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:30,224 HelpFormatter - Program Args: -T CombineVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/txtmp2064756459940712336/Test1-combo-nomnp-mincombine.vcf --rod_priority_list combo,gatk,freebayes --variant:combo /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp.vcf --variant:gatk /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-nomnp.vcf --variant:freebayes /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-freebayes-nomnp.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION --sites_only --minimalVCF | |
| [2014-10-03 19:06] INFO 19:06:30,225 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:30,226 HelpFormatter - Date/Time: 2014/10/03 19:06:30 | |
| [2014-10-03 19:06] INFO 19:06:30,226 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:30,227 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:30,239 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:30,261 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:30,310 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:30,316 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:30,316 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:30,317 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:30,318 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:30,323 CombineVariants - Pre-stripping genotypes for performance | |
| [2014-10-03 19:06] INFO 19:06:30,407 ProgressMeter - done 1.10e+01 0.0 s 2.3 h 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:30,408 ProgressMeter - Total runtime 0.09 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:30,646 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:30,647 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:30,648 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:30,648 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:30,649 HelpFormatter - Program Args: -T SelectVariants --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp-mincombine-fix-consensus.vcf --unsafe ALL --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/txtmp6266268405822761392/Test1-combo-nomnp-mincombine-fix-consensus-cleaned.vcf --excludeNonVariants --excludeFiltered | |
| [2014-10-03 19:06] INFO 19:06:30,650 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:30,650 HelpFormatter - Date/Time: 2014/10/03 19:06:30 | |
| [2014-10-03 19:06] INFO 19:06:30,652 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:30,652 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:30,660 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:30,673 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:30,676 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:30,676 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:30,676 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:30,676 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:30,678 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:30,719 SelectVariants - 11 records processed. | |
| [2014-10-03 19:06] INFO 19:06:30,721 ProgressMeter - done 1.10e+01 0.0 s 67.5 m 84.4% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:30,721 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:30,796 GeneratedMethodAccessor34 - State :compare :: {:desc "Comparing VCFs: combo vs gatk"} | |
| [2014-10-03 19:06] INFO 19:06:30,926 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:30,931 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:30,932 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:30,932 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:30,933 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-nomnp-nosv.vcf --concordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp-mincombine-fix-consensus-cleaned-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp636942943323083141/Test1-gatk-combo-concordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:30,934 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:30,934 HelpFormatter - Date/Time: 2014/10/03 19:06:30 | |
| [2014-10-03 19:06] INFO 19:06:30,935 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:30,936 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:30,951 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:30,978 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:31,002 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:31,003 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:31,004 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:31,004 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:31,005 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:31,006 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:31,008 SelectVariants - Selecting only variants concordant with the track: concordance | |
| [2014-10-03 19:06] INFO 19:06:31,036 SelectVariants - 10 records processed. | |
| [2014-10-03 19:06] INFO 19:06:31,038 ProgressMeter - done 1.10e+01 0.0 s 50.2 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:31,038 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:31,145 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:31,145 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:31,146 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:31,147 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:31,147 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp-mincombine-fix-consensus-cleaned-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp4351625310482094116/Test1-combo-gatk-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:31,148 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:31,148 HelpFormatter - Date/Time: 2014/10/03 19:06:31 | |
| [2014-10-03 19:06] INFO 19:06:31,149 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:31,149 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:31,155 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:31,167 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:31,174 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:31,176 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:31,177 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:31,178 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:31,178 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:31,179 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:31,180 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:06] INFO 19:06:31,212 SelectVariants - 11 records processed. | |
| [2014-10-03 19:06] INFO 19:06:31,214 ProgressMeter - done 1.10e+01 0.0 s 54.2 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:31,214 ProgressMeter - Total runtime 0.04 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:31,327 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:31,328 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:31,328 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:31,328 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:31,329 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp-mincombine-fix-consensus-cleaned-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp3340192524615112838/Test1-gatk-combo-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:31,330 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:31,334 HelpFormatter - Date/Time: 2014/10/03 19:06:31 | |
| [2014-10-03 19:06] INFO 19:06:31,335 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:31,336 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:31,346 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:31,379 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:31,392 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:31,393 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:31,394 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:31,395 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:31,395 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:31,399 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:31,401 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:06] INFO 19:06:31,421 SelectVariants - 10 records processed. | |
| [2014-10-03 19:06] INFO 19:06:31,423 ProgressMeter - done 1.10e+01 0.0 s 42.1 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:31,423 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:31,505 GeneratedMethodAccessor34 - State :compare :: {:desc "Comparing VCFs: combo vs freebayes"} | |
| [2014-10-03 19:06] INFO 19:06:31,609 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:31,610 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:31,611 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:31,611 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:31,612 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-freebayes-nomnp-nosv.vcf --concordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp-mincombine-fix-consensus-cleaned-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp7271454085673156491/Test1-freebayes-combo-concordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:31,612 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:31,613 HelpFormatter - Date/Time: 2014/10/03 19:06:31 | |
| [2014-10-03 19:06] INFO 19:06:31,613 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:31,614 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:31,620 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:31,631 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:31,642 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:31,643 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:31,644 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:31,644 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:31,645 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:31,645 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:31,646 SelectVariants - Selecting only variants concordant with the track: concordance | |
| [2014-10-03 19:06] INFO 19:06:31,672 SelectVariants - 11 records processed. | |
| [2014-10-03 19:06] INFO 19:06:31,676 ProgressMeter - done 1.10e+01 0.0 s 47.9 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:31,677 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:31,782 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:31,791 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:31,792 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:31,792 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:31,793 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp-mincombine-fix-consensus-cleaned-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-freebayes-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp8339062929091199313/Test1-combo-freebayes-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:31,793 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:31,794 HelpFormatter - Date/Time: 2014/10/03 19:06:31 | |
| [2014-10-03 19:06] INFO 19:06:31,795 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:31,795 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:31,802 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:31,841 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:31,846 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:31,850 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:31,851 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:31,852 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:31,852 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:31,855 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:31,856 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:06] INFO 19:06:31,872 SelectVariants - 11 records processed. | |
| [2014-10-03 19:06] INFO 19:06:31,873 ProgressMeter - done 1.10e+01 0.0 s 32.6 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:31,874 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:31,954 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:31,955 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:31,956 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:31,956 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:31,956 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-freebayes-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp-mincombine-fix-consensus-cleaned-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp2672378666053102619/Test1-freebayes-combo-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:31,957 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:31,958 HelpFormatter - Date/Time: 2014/10/03 19:06:31 | |
| [2014-10-03 19:06] INFO 19:06:31,958 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:31,959 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:31,978 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:32,009 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:32,021 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:32,022 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:32,022 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:32,023 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:32,023 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:32,024 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:32,025 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:06] INFO 19:06:32,042 SelectVariants - 11 records processed. | |
| [2014-10-03 19:06] INFO 19:06:32,043 ProgressMeter - done 1.10e+01 0.0 s 31.1 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:32,044 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:32,110 GeneratedMethodAccessor34 - State :compare :: {:desc "Comparing VCFs: gatk vs freebayes"} | |
| [2014-10-03 19:06] INFO 19:06:32,198 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:32,207 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:32,208 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:32,209 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:32,209 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-freebayes-nomnp-nosv.vcf --concordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp6616112356173013950/Test1-freebayes-gatk-concordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:32,210 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:32,210 HelpFormatter - Date/Time: 2014/10/03 19:06:32 | |
| [2014-10-03 19:06] INFO 19:06:32,211 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:32,211 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:32,220 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:32,233 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:32,244 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:32,245 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:32,245 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:32,246 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:32,246 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:32,247 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:32,249 SelectVariants - Selecting only variants concordant with the track: concordance | |
| [2014-10-03 19:06] INFO 19:06:32,265 SelectVariants - 11 records processed. | |
| [2014-10-03 19:06] INFO 19:06:32,267 ProgressMeter - done 1.10e+01 0.0 s 31.8 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:32,267 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:32,358 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:32,358 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:32,359 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:32,359 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:32,360 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-freebayes-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp4655166617242253511/Test1-gatk-freebayes-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:32,360 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:32,361 HelpFormatter - Date/Time: 2014/10/03 19:06:32 | |
| [2014-10-03 19:06] INFO 19:06:32,361 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:32,362 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:32,369 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:32,398 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:32,405 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:32,406 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:32,407 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:32,407 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:32,408 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:32,409 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:32,410 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:06] INFO 19:06:32,423 SelectVariants - 10 records processed. | |
| [2014-10-03 19:06] INFO 19:06:32,424 ProgressMeter - done 1.10e+01 0.0 s 25.6 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:32,425 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:32,516 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:32,516 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:32,517 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:32,518 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:32,518 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-freebayes-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp8577877462399409495/Test1-freebayes-gatk-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:32,519 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:32,519 HelpFormatter - Date/Time: 2014/10/03 19:06:32 | |
| [2014-10-03 19:06] INFO 19:06:32,520 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:32,520 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:32,529 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:32,548 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:32,560 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:32,561 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:32,562 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:32,562 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:32,563 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:32,566 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:32,570 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:06] INFO 19:06:32,596 SelectVariants - 11 records processed. | |
| [2014-10-03 19:06] INFO 19:06:32,598 ProgressMeter - done 1.10e+01 0.0 s 53.8 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:32,600 ProgressMeter - Total runtime 0.04 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:32,667 GeneratedMethodAccessor34 - State :finalize :: {:desc "Finalize multiple: combo"} | |
| [2014-10-03 19:06] INFO 19:06:32,690 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:32,691 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:32,692 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:32,692 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:32,692 HelpFormatter - Program Args: -T CombineVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/multiple/txtmp8456646158300327713/Test1-multiall-fullcombine.vcf --rod_priority_list comboANDgatk,comboANDfreebayes,gatkANDfreebayes --variant:comboANDgatk /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/Test1-gatk-combo-concordance.vcf --variant:comboANDfreebayes /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/Test1-freebayes-combo-concordance.vcf --variant:gatkANDfreebayes /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/Test1-freebayes-gatk-concordance.vcf --genotypemergeoption PRIORITIZE | |
| [2014-10-03 19:06] INFO 19:06:32,693 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:32,694 HelpFormatter - Date/Time: 2014/10/03 19:06:32 | |
| [2014-10-03 19:06] INFO 19:06:32,694 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:32,694 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:32,700 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:32,714 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:32,723 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:32,725 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:32,725 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:32,725 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:32,753 ProgressMeter - done 1.10e+01 0.0 s 41.7 m 84.4% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:32,754 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:32,837 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:32,838 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:32,839 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:32,839 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:32,840 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/multiple/txtmp5943032576575202280/Test1-multiall-fullcombine-Intersection.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/multiple/Test1-multiall-fullcombine.vcf -select set == 'Intersection' | |
| [2014-10-03 19:06] INFO 19:06:32,840 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:32,841 HelpFormatter - Date/Time: 2014/10/03 19:06:32 | |
| [2014-10-03 19:06] INFO 19:06:32,841 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:32,842 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:32,851 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:32,864 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:32,866 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:32,867 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:32,868 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:32,868 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:32,913 SelectVariants - 11 records processed. | |
| [2014-10-03 19:06] INFO 19:06:32,915 ProgressMeter - done 1.10e+01 0.0 s 71.3 m 84.4% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:32,915 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:33,008 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:33,009 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:33,009 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:33,010 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:33,010 HelpFormatter - Program Args: -T CombineVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/multiple/txtmp5469728273956686990/Test1-multinocombo-fullcombine.vcf --rod_priority_list gatkANDfreebayes --variant:gatkANDfreebayes /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/Test1-freebayes-gatk-concordance.vcf --genotypemergeoption PRIORITIZE | |
| [2014-10-03 19:06] INFO 19:06:33,011 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:33,011 HelpFormatter - Date/Time: 2014/10/03 19:06:33 | |
| [2014-10-03 19:06] INFO 19:06:33,012 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:33,012 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:33,016 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:33,028 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:33,031 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:33,035 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:33,035 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:33,036 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:33,067 ProgressMeter - done 1.00e+01 0.0 s 52.8 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:33,068 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:33,166 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:33,166 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:33,168 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:33,168 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:33,169 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/multiple/txtmp3158353071944376258/Test1-multinocombo-fullcombine-Intersection.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/multiple/Test1-multinocombo-fullcombine.vcf -select set == 'Intersection' | |
| [2014-10-03 19:06] INFO 19:06:33,169 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:33,175 HelpFormatter - Date/Time: 2014/10/03 19:06:33 | |
| [2014-10-03 19:06] INFO 19:06:33,176 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:33,177 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:33,187 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:33,219 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:33,224 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:33,225 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:33,225 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:33,226 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:33,253 SelectVariants - 10 records processed. | |
| [2014-10-03 19:06] INFO 19:06:33,259 ProgressMeter - done 1.00e+01 0.0 s 56.7 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:33,263 ProgressMeter - Total runtime 0.04 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:33,425 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:33,431 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:33,432 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:33,433 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:33,433 HelpFormatter - Program Args: -T CombineVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/multiple/txtmp1549847997909701889/Test1-multiall-nocombo-fullcombine.vcf --rod_priority_list truep,combo --variant:truep /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/multiple/Test1-multiall-fullcombine-Intersection.vcf --variant:combo /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/multiple/Test1-multinocombo-fullcombine-Intersection.vcf --genotypemergeoption PRIORITIZE | |
| [2014-10-03 19:06] INFO 19:06:33,434 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:33,434 HelpFormatter - Date/Time: 2014/10/03 19:06:33 | |
| [2014-10-03 19:06] INFO 19:06:33,438 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:33,439 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:33,442 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:33,470 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:33,486 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:33,486 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:33,488 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:33,488 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:33,532 ProgressMeter - done 1.00e+01 0.0 s 74.2 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:33,533 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:33,716 GeneratedMethodAccessor34 - State :finalize :: {:desc "Finalize recal-filter: combo, gatk"} | |
| [2014-10-03 19:06] INFO 19:06:35,315 C3P0Registry - Initializing c3p0-0.9.1.2 [built 21-May-2007 15:04:56; debug? true; trace: 10] | |
| [2014-10-03 19:06] Filter VCF with {{:variant-type :complex, :attr-key :all, :zygosity :het} nil, {:variant-type :complex, :attr-key :all, :zygosity :hom} #<SMO SMO | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] Kernel used: | |
| [2014-10-03 19:06] Linear Kernel: K(x,y) = <x,y> | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] Classifier for classes: pass, fail | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] BinarySMO | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] Machine linear: showing attribute weights, not support vectors. | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] + 1 | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] Number of kernel evaluations: 0 | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] >, {:variant-type :snp, :attr-key :all, :zygosity :het} nil, {:variant-type :snp, :attr-key :all, :zygosity :hom} nil} | |
| [2014-10-03 19:06] Filter VCF with {{:variant-type :complex, :attr-key :calling, :zygosity :het} nil, {:variant-type :complex, :attr-key :calling, :zygosity :hom} #<SMO SMO | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] Kernel used: | |
| [2014-10-03 19:06] Linear Kernel: K(x,y) = <x,y> | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] Classifier for classes: pass, fail | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] BinarySMO | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] Machine linear: showing attribute weights, not support vectors. | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] + 1 | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] Number of kernel evaluations: 0 | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] >, {:variant-type :snp, :attr-key :calling, :zygosity :het} nil, {:variant-type :snp, :attr-key :calling, :zygosity :hom} #<SMO SMO | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] Kernel used: | |
| [2014-10-03 19:06] Linear Kernel: K(x,y) = <x,y> | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] Classifier for classes: pass, fail | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] BinarySMO | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] Machine linear: showing attribute weights, not support vectors. | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] - 1 | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] Number of kernel evaluations: 0 | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] >, {:variant-type :complex, :attr-key :balance, :zygosity :het} nil, {:variant-type :complex, :attr-key :balance, :zygosity :hom} #<SMO SMO | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] Kernel used: | |
| [2014-10-03 19:06] Linear Kernel: K(x,y) = <x,y> | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] Classifier for classes: pass, fail | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] BinarySMO | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] Machine linear: showing attribute weights, not support vectors. | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] + 1 | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] Number of kernel evaluations: 0 | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] >, {:variant-type :snp, :attr-key :balance, :zygosity :het} nil, {:variant-type :snp, :attr-key :balance, :zygosity :hom} #<SMO SMO | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] Kernel used: | |
| [2014-10-03 19:06] Linear Kernel: K(x,y) = <x,y> | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] Classifier for classes: pass, fail | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] BinarySMO | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] Machine linear: showing attribute weights, not support vectors. | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] - 1 | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] Number of kernel evaluations: 0 | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] >} | |
| [2014-10-03 19:06] INFO 19:06:39,902 GeneratedMethodAccessor34 - State :compare :: {:desc "Comparing VCFs: combo-recal vs gatk"} | |
| [2014-10-03 19:06] INFO 19:06:39,952 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:39,955 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:39,955 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:39,956 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:39,956 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-nomnp-nosv.vcf --concordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp-mincombine-fix-consensus-cleaned-nosv-nofilter-cfilter.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp8058279075248783512/Test1-gatk-combo-recal-concordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:39,957 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:39,958 HelpFormatter - Date/Time: 2014/10/03 19:06:39 | |
| [2014-10-03 19:06] INFO 19:06:39,958 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:39,959 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:39,972 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:40,001 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:40,019 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:40,019 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:40,020 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:40,021 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:40,021 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:40,028 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:40,030 SelectVariants - Selecting only variants concordant with the track: concordance | |
| [2014-10-03 19:06] INFO 19:06:40,058 SelectVariants - 10 records processed. | |
| [2014-10-03 19:06] INFO 19:06:40,068 ProgressMeter - done 1.10e+01 0.0 s 71.4 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:40,071 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:40,197 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:40,197 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:40,197 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:40,198 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:40,198 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp-mincombine-fix-consensus-cleaned-nosv-nofilter-cfilter.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp7986215488559333017/Test1-combo-recal-gatk-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:40,199 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:40,200 HelpFormatter - Date/Time: 2014/10/03 19:06:40 | |
| [2014-10-03 19:06] INFO 19:06:40,200 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:40,201 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:40,212 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:40,228 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:40,231 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:40,231 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:40,231 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:40,232 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:40,232 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:40,235 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:40,237 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:06] INFO 19:06:40,248 SelectVariants - 11 records processed. | |
| [2014-10-03 19:06] INFO 19:06:40,250 ProgressMeter - done 1.10e+01 0.0 s 27.1 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:40,250 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:40,340 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:40,345 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:40,345 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:40,346 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:40,347 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-gatk-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/prep/Test1-combo-nomnp-mincombine-fix-consensus-cleaned-nosv-nofilter-cfilter.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble-work/txtmp9204360168389149547/Test1-gatk-combo-recal-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:40,347 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:40,348 HelpFormatter - Date/Time: 2014/10/03 19:06:40 | |
| [2014-10-03 19:06] INFO 19:06:40,348 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:40,349 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:40,352 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:40,368 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:40,373 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:40,374 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:40,374 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:40,375 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:40,375 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:40,376 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:40,377 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:06] INFO 19:06:40,396 SelectVariants - 10 records processed. | |
| [2014-10-03 19:06] INFO 19:06:40,397 ProgressMeter - done 1.10e+01 0.0 s 34.3 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:40,398 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:40,479 GeneratedMethodAccessor34 - State :summary :: {:desc "Summarize comparisons"} | |
| [2014-10-03 19:06] INFO 19:06:40,656 GeneratedMethodAccessor34 - State :finished :: {:desc "Finished"} | |
| [2014-10-03 19:06] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:06] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:06] Comparing variant calls using bcbio.variation : Test1 | |
| [2014-10-03 19:06] 2014-10-03 19:06:43,527 [INFO ] MLog clients using log4j logging. | |
| [2014-10-03 19:06] 2014-10-03 19:06:43,773 [INFO ] State :begin :: {:desc "Starting variation analysis"} | |
| [2014-10-03 19:06] 2014-10-03 19:06:43,800 [INFO ] State :clean :: {:desc "Cleaning input VCF: ref"} | |
| [2014-10-03 19:06] 2014-10-03 19:06:43,999 [INFO ] State :merge :: {:desc "Merging multiple input files: ref"} | |
| [2014-10-03 19:06] 2014-10-03 19:06:44,000 [INFO ] State :prep :: {:desc "Prepare VCF, resorting to genome build: ref"} | |
| [2014-10-03 19:06] INFO 19:06:46,888 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:46,889 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:46,890 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:46,891 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:46,893 HelpFormatter - Program Args: -T SelectVariants --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-ref-prep.vcf --unsafe ALL --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/txtmp645783135218942002/Test1-ref-noref.vcf --excludeNonVariants --excludeFiltered -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:46,896 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:46,897 HelpFormatter - Date/Time: 2014/10/03 19:06:46 | |
| [2014-10-03 19:06] INFO 19:06:46,897 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:46,898 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:47,453 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:47,515 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:47,530 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:47,566 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:47,567 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:47,568 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:47,569 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:47,572 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:47,636 SelectVariants - 9 records processed. | |
| [2014-10-03 19:06] INFO 19:06:47,639 ProgressMeter - done 9.00e+00 0.0 s 2.2 h 1.0% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:47,640 ProgressMeter - Total runtime 0.07 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:47,735 NativeMethodAccessorImpl - State :normalize :: {:desc "Normalize MNP and indel variants: ref"} | |
| [2014-10-03 19:06] INFO 19:06:47,796 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:47,797 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:47,798 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:47,798 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:47,800 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/txtmp822098963536454552/Test1-ref-noref-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-ref-noref.vcf | |
| [2014-10-03 19:06] INFO 19:06:47,800 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:47,801 HelpFormatter - Date/Time: 2014/10/03 19:06:47 | |
| [2014-10-03 19:06] INFO 19:06:47,801 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:47,802 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:47,809 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:47,827 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:47,838 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:47,839 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:47,840 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:47,840 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] 0 variants were aligned | |
| [2014-10-03 19:06] INFO 19:06:47,884 ProgressMeter - done 9.00e+00 0.0 s 81.5 m 0.4% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:47,885 ProgressMeter - Total runtime 0.04 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:48,044 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:48,047 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:48,048 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:48,049 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:48,049 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/txtmp252937286723103204/Test1-ref-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-ref-worknomnp.vcf | |
| [2014-10-03 19:06] INFO 19:06:48,050 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:48,050 HelpFormatter - Date/Time: 2014/10/03 19:06:48 | |
| [2014-10-03 19:06] INFO 19:06:48,051 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:48,051 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:48,061 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:48,091 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:48,094 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:48,095 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:48,095 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:48,095 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] 0 variants were aligned | |
| [2014-10-03 19:06] INFO 19:06:48,112 ProgressMeter - done 9.00e+00 0.0 s 30.9 m 0.4% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:48,112 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:48,174 NativeMethodAccessorImpl - State :clean :: {:desc "Cleaning input VCF: eval"} | |
| [2014-10-03 19:06] INFO 19:06:48,175 NativeMethodAccessorImpl - State :merge :: {:desc "Merging multiple input files: eval"} | |
| [2014-10-03 19:06] INFO 19:06:48,176 NativeMethodAccessorImpl - State :prep :: {:desc "Prepare VCF, resorting to genome build: eval"} | |
| [2014-10-03 19:06] INFO 19:06:48,256 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:48,257 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:48,258 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:48,263 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:48,264 HelpFormatter - Program Args: -T SelectVariants --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/ensemble/TestBatch1/TestBatch1-ensemble.vcf --unsafe ALL --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/txtmp3805018689501243804/Test1-eval-noref.vcf --excludeNonVariants --excludeFiltered -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:48,265 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:48,265 HelpFormatter - Date/Time: 2014/10/03 19:06:48 | |
| [2014-10-03 19:06] INFO 19:06:48,266 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:48,267 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:48,281 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:48,301 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:48,306 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:48,308 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:48,308 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:48,309 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:48,310 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:48,310 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:48,378 SelectVariants - 11 records processed. | |
| [2014-10-03 19:06] INFO 19:06:48,380 ProgressMeter - done 1.10e+01 0.0 s 107.5 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:48,381 ProgressMeter - Total runtime 0.07 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:48,463 NativeMethodAccessorImpl - State :normalize :: {:desc "Normalize MNP and indel variants: eval"} | |
| [2014-10-03 19:06] INFO 19:06:48,512 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:48,513 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:48,513 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:48,513 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:48,514 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/txtmp8949097817996181075/Test1-eval-noref-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-eval-noref.vcf | |
| [2014-10-03 19:06] INFO 19:06:48,514 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:48,515 HelpFormatter - Date/Time: 2014/10/03 19:06:48 | |
| [2014-10-03 19:06] INFO 19:06:48,515 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:48,515 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:48,520 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:48,539 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:48,542 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:48,543 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:48,543 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:48,544 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] 0 variants were aligned | |
| [2014-10-03 19:06] INFO 19:06:48,573 ProgressMeter - done 1.00e+01 0.0 s 49.7 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:48,574 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:48,708 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:48,711 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:48,712 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:48,712 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:48,713 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/txtmp3996053681371912613/Test1-eval-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-eval-worknomnp.vcf | |
| [2014-10-03 19:06] INFO 19:06:48,714 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:48,714 HelpFormatter - Date/Time: 2014/10/03 19:06:48 | |
| [2014-10-03 19:06] INFO 19:06:48,715 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:48,715 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:48,725 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:48,754 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:48,769 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:48,770 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:48,771 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:48,773 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] 0 variants were aligned | |
| [2014-10-03 19:06] INFO 19:06:48,804 ProgressMeter - done 1.00e+01 0.0 s 54.8 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:48,805 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:48,885 NativeMethodAccessorImpl - State :combine :: {:desc "Creating merged VCF files for all comparisons"} | |
| [2014-10-03 19:06] INFO 19:06:48,887 NativeMethodAccessorImpl - State :annotate :: {:desc "Annotate VCFs with metrics"} | |
| [2014-10-03 19:06] INFO 19:06:48,888 NativeMethodAccessorImpl - State :filter :: {:desc "Post annotation filtering"} | |
| [2014-10-03 19:06] INFO 19:06:48,896 NativeMethodAccessorImpl - State :compare :: {:desc "Comparing VCFs: ref vs eval"} | |
| [2014-10-03 19:06] INFO 19:06:49,106 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:49,108 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:49,109 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:49,109 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:49,110 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-eval-nomnp-nosv.vcf --concordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-ref-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/txtmp5708651125972171038/Test1-eval-ref-concordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:49,110 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:49,111 HelpFormatter - Date/Time: 2014/10/03 19:06:49 | |
| [2014-10-03 19:06] INFO 19:06:49,111 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:49,112 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:49,118 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:49,130 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:49,142 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:49,143 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:49,144 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:49,144 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:49,145 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:49,145 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:49,150 SelectVariants - Selecting only variants concordant with the track: concordance | |
| [2014-10-03 19:06] INFO 19:06:49,185 SelectVariants - 10 records processed. | |
| [2014-10-03 19:06] INFO 19:06:49,192 ProgressMeter - done 1.00e+01 0.0 s 79.7 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:49,193 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:49,308 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:49,309 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:49,309 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:49,310 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:49,310 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-ref-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-eval-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/txtmp2161643031565518350/Test1-ref-eval-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:49,311 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:49,311 HelpFormatter - Date/Time: 2014/10/03 19:06:49 | |
| [2014-10-03 19:06] INFO 19:06:49,312 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:49,312 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:49,321 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:49,334 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:49,341 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:49,342 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:49,342 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:49,344 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:49,345 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:49,346 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:49,349 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:06] INFO 19:06:49,363 SelectVariants - 9 records processed. | |
| [2014-10-03 19:06] INFO 19:06:49,365 ProgressMeter - done 1.00e+01 0.0 s 34.3 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:49,365 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:49,454 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:49,455 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:49,455 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:49,456 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:49,457 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-eval-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/prep/Test1-ref-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/txtmp840909584576520369/Test1-eval-ref-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:06] INFO 19:06:49,457 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:49,458 HelpFormatter - Date/Time: 2014/10/03 19:06:49 | |
| [2014-10-03 19:06] INFO 19:06:49,458 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:49,459 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:49,465 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:49,476 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:49,484 IntervalUtils - Processing 5057 bp from intervals | |
| [2014-10-03 19:06] INFO 19:06:49,485 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:49,486 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:49,486 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:49,487 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:49,487 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:06] INFO 19:06:49,489 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:06] INFO 19:06:49,505 SelectVariants - 10 records processed. | |
| [2014-10-03 19:06] INFO 19:06:49,507 ProgressMeter - done 1.00e+01 0.0 s 33.7 m 98.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:49,507 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:49,612 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:49,616 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:49,616 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:49,617 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:49,617 HelpFormatter - Program Args: -T VariantAnnotator --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/7_100326_FC6107FAAXX-sort.bam --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/Test1-ref-eval-discordance-asref.vcf --allow_potentially_misencoded_quality_scores -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/txtmp5670723695596433587/Test1-ref-eval-discordance-asref-annotated.vcf -A DepthOfCoverage -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/Test1-ref-eval-discordance-asref.vcf | |
| [2014-10-03 19:06] INFO 19:06:49,618 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:49,619 HelpFormatter - Date/Time: 2014/10/03 19:06:49 | |
| [2014-10-03 19:06] INFO 19:06:49,619 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:49,620 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:49,629 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:49,649 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 | |
| [2014-10-03 19:06] INFO 19:06:49,651 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 19:06] INFO 19:06:49,653 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.00 | |
| [2014-10-03 19:06] WARN 19:06:49,658 IntervalUtils - The interval file /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/Test1-ref-eval-discordance-asref.vcf contains no intervals that could be parsed. | |
| [2014-10-03 19:06] INFO 19:06:49,658 IntervalUtils - Processing 0 bp from intervals | |
| [2014-10-03 19:06] WARN 19:06:49,659 GenomeAnalysisEngine - The given combination of -L and -XL options results in an empty set. No intervals to process. | |
| [2014-10-03 19:06] INFO 19:06:49,660 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 19:06] INFO 19:06:49,668 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:49,668 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:49,669 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:49,701 VariantAnnotator - Processed 0 loci. | |
| [2014-10-03 19:06] | |
| [2014-10-03 19:06] INFO 19:06:49,705 ProgressMeter - done 0.00e+00 0.0 s 10.2 h 0.0% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:49,706 ProgressMeter - Total runtime 0.04 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:49,820 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:49,821 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:06] INFO 19:06:49,822 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:06] INFO 19:06:49,822 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:06] INFO 19:06:49,827 HelpFormatter - Program Args: -T CombineVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/txtmp1962129883701251159/Test1-eval-ref-discordance-fullcombine.vcf --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null --variant:v0 /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/Test1-eval-ref-discordance.vcf --variant:v1 /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/Test1-ref-eval-discordance-asref-annotated.vcf --genotypemergeoption PRIORITIZE | |
| [2014-10-03 19:06] INFO 19:06:49,828 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:06] INFO 19:06:49,829 HelpFormatter - Date/Time: 2014/10/03 19:06:49 | |
| [2014-10-03 19:06] INFO 19:06:49,829 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:49,830 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:06] INFO 19:06:49,837 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:06] INFO 19:06:49,858 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:06] INFO 19:06:49,869 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:49,869 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:06] INFO 19:06:49,870 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:06] INFO 19:06:49,870 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:06] INFO 19:06:49,892 ProgressMeter - done 1.00e+00 0.0 s 5.7 h 84.7% 0.0 s 0.0 s | |
| [2014-10-03 19:06] INFO 19:06:49,893 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:06] INFO 19:06:49,973 NativeMethodAccessorImpl - State :summary :: {:desc "Summarize comparisons"} | |
| [2014-10-03 19:06] INFO 19:06:50,923 C3P0Registry - Initializing c3p0-0.9.1.2 [built 21-May-2007 15:04:56; debug? true; trace: 10] | |
| [2014-10-03 19:06] INFO 19:06:51,007 AbstractPoolBackedDataSource - Initializing c3p0 pool... com.mchange.v2.c3p0.ComboPooledDataSource [ acquireIncrement -> 3, acquireRetryAttempts -> 30, acquireRetryDelay -> 1000, autoCommitOnClose -> false, automaticTestTable -> null, breakAfterAcquireFailure -> false, checkoutTimeout -> 0, connectionCustomizerClassName -> null, connectionTesterClassName -> com.mchange.v2.c3p0.impl.DefaultConnectionTester, dataSourceName -> 2rvy8f941nrn89zpxsqlm|2bfa016, debugUnreturnedConnectionStackTraces -> false, description -> null, driverClass -> org.sqlite.JDBC, factoryClassLocation -> null, forceIgnoreUnresolvedTransactions -> false, identityToken -> 2rvy8f941nrn89zpxsqlm|2bfa016, idleConnectionTestPeriod -> 0, initialPoolSize -> 3, jdbcUrl -> jdbc:sqlite:/home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/ensemble/work/Test1-eval-ref-discordance-annotate-gemini.db, maxAdministrativeTaskTime -> 0, maxConnectionAge -> 0, maxIdleTime -> 0, maxIdleTimeExcessConnections -> 0, maxPoolSize -> 15, maxStatements -> 0, maxStatementsPerConnection -> 0, minPoolSize -> 3, numHelperThreads -> 3, numThreadsAwaitingCheckoutDefaultUser -> 0, preferredTestQuery -> null, properties -> {}, propertyCycle -> 0, testConnectionOnCheckin -> false, testConnectionOnCheckout -> false, unreturnedConnectionTimeout -> 0, usesTraditionalReflectiveProxies -> false ] | |
| [2014-10-03 19:06] INFO 19:06:51,224 NativeMethodAccessorImpl - State :finished :: {:desc "Finished"} | |
| [2014-10-03 19:06] Timing: validation summary | |
| /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/pandas/core/frame.py:1706: UserWarning: Boolean Series key will be reindexed to match DataFrame index. | |
| "DataFrame index.", UserWarning) | |
| [2014-10-03 19:06] Timing: structural variation | |
| [2014-10-03 19:06] Timing: population database | |
| [2014-10-03 19:06] multiprocessing: prep_gemini_db | |
| [2014-10-03 19:06] Timing: quality control | |
| [2014-10-03 19:06] multiprocessing: pipeline_summary | |
| [2014-10-03 19:06] Generating summary files: ['', 'Test1'] | |
| [2014-10-03 19:06] FastQC: Test1 | |
| [2014-10-03 19:06] Started analysis of 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] Approx 5% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] Approx 10% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] Approx 15% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] Approx 20% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] Approx 25% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] Approx 30% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] Approx 35% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] Approx 40% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] Approx 45% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] Approx 50% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] Approx 55% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] Approx 60% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] Approx 65% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] Approx 70% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] Approx 75% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] Approx 80% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] Approx 85% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] Approx 90% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] Approx 95% complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] Analysis complete for 7_100326_FC6107FAAXX-sort-prep.bam | |
| [2014-10-03 19:06] bamtools stats : Test1 | |
| [2014-10-03 19:06] There is no qsignature for this species: hg19 | |
| [2014-10-03 19:06] multiprocessing: qsignature_summary | |
| [2014-10-03 19:06] Timing: archive | |
| [2014-10-03 19:06] Timing: finished | |
| [2014-10-03 19:06] Storing directory in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/qc | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-ready.bam | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-ready.bam.bai | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-disc.bam | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-disc.bam.bai | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-sr.bam | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-sr.bam.bai | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-ensemble.vcf | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-gatk.vcf.gz | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-gatk.vcf.gz.tbi | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-freebayes.vcf.gz | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-freebayes.vcf.gz.tbi | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-validate.pdf | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/100326_FC6107FAAXX/programs.txt | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/100326_FC6107FAAXX/bcbio-nextgen.log | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/100326_FC6107FAAXX/bcbio-nextgen-commands.log | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/100326_FC6107FAAXX/project-summary.yaml | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/100326_FC6107FAAXX/TestBatch1-ensemble.vcf | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/100326_FC6107FAAXX/TestBatch1-gatk.vcf.gz | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/100326_FC6107FAAXX/TestBatch1-gatk.vcf.gz.tbi | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/100326_FC6107FAAXX/TestBatch1-freebayes.vcf.gz | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/100326_FC6107FAAXX/TestBatch1-freebayes.vcf.gz.tbi | |
| [2014-10-03 19:06] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/100326_FC6107FAAXX/grading-summary.csv | |
| ok | |
| Allow BAM files as input to pipeline. ... [2014-10-03 19:07] Using input YAML configuration: /home/vagrant/bcbio-nextgen/tests/data/automated/run_info-bam.yaml | |
| [2014-10-03 19:07] Checking sample YAML configuration: /home/vagrant/bcbio-nextgen/tests/data/automated/run_info-bam.yaml | |
| [2014-10-03 19:07] Testing minimum versions of installed programs | |
| [2014-10-03 19:07] Resource requests: bwa, sambamba, samtools; memory: 2.0; cores: 16, 1, 16 | |
| [2014-10-03 19:07] Configuring 1 jobs to run, using 1 cores each with 2.2g of memory reserved for each job | |
| [2014-10-03 19:07] Timing: alignment preparation | |
| [2014-10-03 19:07] multiprocessing: prep_align_inputs | |
| [2014-10-03 19:07] BAM to bgzipped fastq | |
| [2014-10-03 19:07] [V] 80349 | |
| [2014-10-03 19:07] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:07] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:07] Index input with grabix: 7_100326_FC6107FAAXX-1.fq.gz | |
| [2014-10-03 19:07] Index input with grabix: 7_100326_FC6107FAAXX-2.fq.gz | |
| [2014-10-03 19:07] Timing: alignment | |
| [2014-10-03 19:07] multiprocessing: process_alignment | |
| [2014-10-03 19:07] Aligning lane Test1 with bwa aligner | |
| [2014-10-03 19:07] bwa mem alignment from fastq: Test1 | |
| [2014-10-03 19:07] samblaster: Version 0.1.20 | |
| [2014-10-03 19:07] samblaster: Inputting from stdin | |
| [2014-10-03 19:07] samblaster: Outputting to stdout | |
| [2014-10-03 19:07] samblaster: Opening /dev/fd/62 for write. | |
| [2014-10-03 19:07] samblaster: Opening /dev/fd/63 for write. | |
| [2014-10-03 19:07] [M::mem_pestat] skip orientation FF as there are not enough pairs | |
| [2014-10-03 19:07] [M::mem_pestat] analyzing insert size distribution for orientation FR... | |
| [2014-10-03 19:07] [M::mem_pestat] (25, 50, 75) percentile: (128, 148, 174) | |
| [2014-10-03 19:07] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (36, 266) | |
| [2014-10-03 19:07] [M::mem_pestat] mean and std.dev: (150.33, 30.95) | |
| [2014-10-03 19:07] [M::mem_pestat] low and high boundaries for proper pairs: (1, 312) | |
| [2014-10-03 19:07] [M::mem_pestat] skip orientation RF as there are not enough pairs | |
| [2014-10-03 19:07] [M::mem_pestat] skip orientation RR as there are not enough pairs | |
| [2014-10-03 19:07] samblaster: Loaded 2 header sequence entries. | |
| [2014-10-03 19:07] [main] Version: 0.7.10-r789 | |
| [2014-10-03 19:07] [main] CMD: /usr/local/bin/bwa mem -M -t 1 -R @RG\tID:7\tPL:illumina\tPU:Test1\tSM:Test1 -v 1 /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fa /dev/fd/63 /dev/fd/62 | |
| [2014-10-03 19:07] [main] Real time: 0.505 sec; CPU: 0.401 sec | |
| [2014-10-03 19:07] samblaster: Output 0 discordant read pairs to /dev/fd/62 | |
| [2014-10-03 19:07] samblaster: Output 2 split reads to /dev/fd/63 | |
| [2014-10-03 19:07] samblaster: Marked 803 of 15000 (5.35%) read ids as duplicates using 1580k memory in 0.014S CPU seconds and 1S wall time. | |
| [2014-10-03 19:07] Index BAM file: Test1-sort-1_60000.bam | |
| [2014-10-03 19:07] Index BAM file: Test1-sort-1_60000-sr.bam | |
| [2014-10-03 19:07] Index BAM file: Test1-sort-1_60000-disc.bam | |
| [2014-10-03 19:07] Aligning lane Test1 with bwa aligner | |
| [2014-10-03 19:07] bwa mem alignment from fastq: Test1 | |
| [2014-10-03 19:07] samblaster: Version 0.1.20 | |
| [2014-10-03 19:07] samblaster: Inputting from stdin | |
| [2014-10-03 19:07] samblaster: Outputting to stdout | |
| [2014-10-03 19:07] samblaster: Opening /dev/fd/62 for write. | |
| [2014-10-03 19:07] samblaster: Opening /dev/fd/63 for write. | |
| [2014-10-03 19:07] [M::mem_pestat] skip orientation FF as there are not enough pairs | |
| [2014-10-03 19:07] [M::mem_pestat] analyzing insert size distribution for orientation FR... | |
| [2014-10-03 19:07] [M::mem_pestat] (25, 50, 75) percentile: (129, 150, 175) | |
| [2014-10-03 19:07] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (37, 267) | |
| [2014-10-03 19:07] [M::mem_pestat] mean and std.dev: (151.92, 31.15) | |
| [2014-10-03 19:07] [M::mem_pestat] low and high boundaries for proper pairs: (1, 313) | |
| [2014-10-03 19:07] [M::mem_pestat] skip orientation RF as there are not enough pairs | |
| [2014-10-03 19:07] [M::mem_pestat] skip orientation RR as there are not enough pairs | |
| [2014-10-03 19:07] samblaster: Loaded 2 header sequence entries. | |
| [2014-10-03 19:07] [main] Version: 0.7.10-r789 | |
| [2014-10-03 19:07] [main] CMD: /usr/local/bin/bwa mem -M -t 1 -R @RG\tID:7\tPL:illumina\tPU:Test1\tSM:Test1 -v 1 /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fa /dev/fd/63 /dev/fd/62 | |
| [2014-10-03 19:07] [main] Real time: 0.494 sec; CPU: 0.404 sec | |
| [2014-10-03 19:07] samblaster: Output 2 discordant read pairs to /dev/fd/62 | |
| [2014-10-03 19:07] samblaster: Output 2 split reads to /dev/fd/63 | |
| [2014-10-03 19:07] samblaster: Marked 735 of 15000 (4.90%) read ids as duplicates using 1576k memory in 0.014S CPU seconds and 1S wall time. | |
| [2014-10-03 19:07] Index BAM file: Test1-sort-60000_119999.bam | |
| [2014-10-03 19:07] Index BAM file: Test1-sort-60000_119999-sr.bam | |
| [2014-10-03 19:07] Index BAM file: Test1-sort-60000_119999-disc.bam | |
| [2014-10-03 19:07] Aligning lane Test1 with bwa aligner | |
| [2014-10-03 19:07] bwa mem alignment from fastq: Test1 | |
| [2014-10-03 19:07] samblaster: Version 0.1.20 | |
| [2014-10-03 19:07] samblaster: Inputting from stdin | |
| [2014-10-03 19:07] samblaster: Outputting to stdout | |
| [2014-10-03 19:07] samblaster: Opening /dev/fd/62 for write. | |
| [2014-10-03 19:07] samblaster: Opening /dev/fd/63 for write. | |
| [2014-10-03 19:07] [M::mem_pestat] skip orientation FF as there are not enough pairs | |
| [2014-10-03 19:07] [M::mem_pestat] analyzing insert size distribution for orientation FR... | |
| [2014-10-03 19:07] [M::mem_pestat] (25, 50, 75) percentile: (130, 151, 176) | |
| [2014-10-03 19:07] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (38, 268) | |
| [2014-10-03 19:07] [M::mem_pestat] mean and std.dev: (152.52, 31.30) | |
| [2014-10-03 19:07] [M::mem_pestat] low and high boundaries for proper pairs: (1, 314) | |
| [2014-10-03 19:07] [M::mem_pestat] skip orientation RF as there are not enough pairs | |
| [2014-10-03 19:07] [M::mem_pestat] skip orientation RR as there are not enough pairs | |
| [2014-10-03 19:07] samblaster: Loaded 2 header sequence entries. | |
| [2014-10-03 19:07] [main] Version: 0.7.10-r789 | |
| [2014-10-03 19:07] [main] CMD: /usr/local/bin/bwa mem -M -t 1 -R @RG\tID:7\tPL:illumina\tPU:Test1\tSM:Test1 -v 1 /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fa /dev/fd/63 /dev/fd/62 | |
| [2014-10-03 19:07] [main] Real time: 0.322 sec; CPU: 0.257 sec | |
| [2014-10-03 19:07] samblaster: Output 3 discordant read pairs to /dev/fd/62 | |
| [2014-10-03 19:07] samblaster: Output 0 split reads to /dev/fd/63 | |
| [2014-10-03 19:07] samblaster: Marked 517 of 10164 (5.09%) read ids as duplicates using 1332k memory in 0.000S CPU seconds and 0S wall time. | |
| [2014-10-03 19:07] Index BAM file: Test1-sort-120000_160655.bam | |
| [2014-10-03 19:07] Index BAM file: Test1-sort-120000_160655-sr.bam | |
| [2014-10-03 19:07] Index BAM file: Test1-sort-120000_160655-disc.bam | |
| [2014-10-03 19:07] multiprocessing: delayed_bam_merge | |
| [2014-10-03 19:07] Merge bam files to Test1-sort-sr.bam | |
| [2014-10-03 19:07] Index BAM file: Test1-sort-sr.bam | |
| [2014-10-03 19:07] Merge bam files to Test1-sort-disc.bam | |
| [2014-10-03 19:07] Index BAM file: Test1-sort-disc.bam | |
| [2014-10-03 19:07] Merge bam files to Test1-sort.bam | |
| [2014-10-03 19:07] Index BAM file: Test1-sort.bam | |
| [2014-10-03 19:07] Timing: callable regions | |
| [2014-10-03 19:07] multiprocessing: prep_samples | |
| [2014-10-03 19:07] Prepare cleaned BED file : Test1 | |
| [2014-10-03 19:07] bgzip variant_regions-bam.bed | |
| [2014-10-03 19:07] tabix index variant_regions-bam.bed.gz | |
| [2014-10-03 19:07] Prepare merged BED file : Test1 | |
| [2014-10-03 19:07] bgzip variant_regions-bam-merged.bed | |
| [2014-10-03 19:07] tabix index variant_regions-bam-merged.bed.gz | |
| [2014-10-03 19:07] multiprocessing: postprocess_alignment | |
| [2014-10-03 19:07] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:07] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:07] multiprocessing: calc_callable_loci | |
| [2014-10-03 19:07] bedtools genomecov: chrM : Test1-sort.bam | |
| [2014-10-03 19:07] bedtools genomecov: chr22 : Test1-sort.bam | |
| [2014-10-03 19:07] multiprocessing: combine_bed | |
| [2014-10-03 19:07] multiprocessing: combine_sample_regions | |
| [2014-10-03 19:07] Identified 4 parallel analysis blocks | |
| Block sizes: | |
| min: 372 | |
| 5%: 466.2 | |
| 25%: 843.0 | |
| median: 2000.0 | |
| 75%: 5874.0 | |
| 95%: 12771.6 | |
| 99%: 14151.12 | |
| max: 14496 | |
| Between block sizes: | |
| min: 632 | |
| 5%: 650.4 | |
| 25%: 724.0 | |
| median: 816.0 | |
| 75%: 908.0 | |
| 95%: 981.6 | |
| 99%: 996.32 | |
| max: 1000 | |
| [2014-10-03 19:07] Timing: coverage | |
| [2014-10-03 19:07] multiprocessing: coverage_summary | |
| [2014-10-03 19:07] Prep chanjo database | |
| [2014-10-03 19:07] Chanjo coverage : Test1 | |
| [2014-10-03 19:07] Resource requests: freebayes, gatk, picard; memory: 2.0, 3.5, 3.5; cores: 1, 1, 1 | |
| [2014-10-03 19:07] Configuring 1 jobs to run, using 1 cores each with 3.8g of memory reserved for each job | |
| [2014-10-03 19:07] Timing: alignment post-processing | |
| [2014-10-03 19:07] multiprocessing: piped_bamprep | |
| [2014-10-03 19:07] Timing: variant calling | |
| [2014-10-03 19:07] multiprocessing: variantcall_sample | |
| [2014-10-03 19:07] Genotyping with FreeBayes | |
| [2014-10-03 19:07] tabix index TestBatch1-chrM_0_1000-raw.vcf.gz | |
| [2014-10-03 19:07] GATK: VariantAnnotator | |
| [2014-10-03 19:07] INFO 19:07:10,248 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:10,250 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 19:07] INFO 19:07:10,250 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:07] INFO 19:07:10,251 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:07] INFO 19:07:10,253 HelpFormatter - Program Args: -T VariantAnnotator -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chrM/TestBatch1-chrM_0_1000-raw.vcf.gz --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/tmptest/bcbiotx/78ba1786-4b30-11e4-9a0e-080027201064/tmpitQuhp/TestBatch1-chrM_0_1000-raw-gatkann.vcf.gz -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chrM/TestBatch1-chrM_0_1000-raw.vcf.gz --dbsnp /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality -A DepthPerAlleleBySample -A Coverage --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment | |
| [2014-10-03 19:07] INFO 19:07:10,256 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:07] INFO 19:07:10,256 HelpFormatter - Date/Time: 2014/10/03 19:07:10 | |
| [2014-10-03 19:07] INFO 19:07:10,257 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:10,258 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:10,764 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:07] INFO 19:07:10,830 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 | |
| [2014-10-03 19:07] INFO 19:07:10,836 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 19:07] INFO 19:07:10,844 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 19:07] INFO 19:07:10,902 IntervalUtils - Processing 4 bp from intervals | |
| [2014-10-03 19:07] WARN 19:07:10,905 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:07] WARN 19:07:10,911 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:07] INFO 19:07:10,978 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 19:07] INFO 19:07:10,993 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:10,996 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:07] INFO 19:07:10,996 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 19:07] INFO 19:07:10,997 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 19:07] INFO 19:07:11,630 VariantAnnotator - Processed 4 loci. | |
| [2014-10-03 19:07] | |
| [2014-10-03 19:07] INFO 19:07:11,646 ProgressMeter - done 10.0 0.0 s 18.0 h 75.0% 0.0 s 0.0 s | |
| [2014-10-03 19:07] INFO 19:07:11,647 ProgressMeter - Total runtime 0.65 secs, 0.01 min, 0.00 hours | |
| [2014-10-03 19:07] INFO 19:07:11,648 MicroScheduler - 113 reads were filtered out during the traversal out of approximately 2454 total reads (4.60%) | |
| [2014-10-03 19:07] INFO 19:07:11,649 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 19:07] INFO 19:07:11,650 MicroScheduler - -> 113 reads (4.60% of total) failing DuplicateReadFilter | |
| [2014-10-03 19:07] INFO 19:07:11,651 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter | |
| [2014-10-03 19:07] INFO 19:07:11,651 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 19:07] INFO 19:07:11,652 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 19:07] INFO 19:07:11,653 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter | |
| [2014-10-03 19:07] INFO 19:07:18,072 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 19:07] Genotyping with FreeBayes | |
| [2014-10-03 19:07] tabix index TestBatch1-chrM_2000_5000-raw.vcf.gz | |
| [2014-10-03 19:07] GATK: VariantAnnotator | |
| [2014-10-03 19:07] INFO 19:07:20,955 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:20,957 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 19:07] INFO 19:07:20,958 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:07] INFO 19:07:20,958 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:07] INFO 19:07:20,962 HelpFormatter - Program Args: -T VariantAnnotator -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chrM/TestBatch1-chrM_2000_5000-raw.vcf.gz --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/tmptest/bcbiotx/7f27fc50-4b30-11e4-9a0e-080027201064/tmpwsa8ZM/TestBatch1-chrM_2000_5000-raw-gatkann.vcf.gz -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chrM/TestBatch1-chrM_2000_5000-raw.vcf.gz --dbsnp /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality -A DepthPerAlleleBySample -A Coverage --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment | |
| [2014-10-03 19:07] INFO 19:07:20,964 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:07] INFO 19:07:20,965 HelpFormatter - Date/Time: 2014/10/03 19:07:20 | |
| [2014-10-03 19:07] INFO 19:07:20,966 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:20,966 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:21,529 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:07] INFO 19:07:21,599 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 | |
| [2014-10-03 19:07] INFO 19:07:21,604 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 19:07] INFO 19:07:21,612 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 19:07] INFO 19:07:21,671 IntervalUtils - Processing 5 bp from intervals | |
| [2014-10-03 19:07] WARN 19:07:21,674 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:07] WARN 19:07:21,678 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:07] INFO 19:07:21,746 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 19:07] INFO 19:07:21,763 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:21,764 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:07] INFO 19:07:21,765 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 19:07] INFO 19:07:21,767 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 19:07] INFO 19:07:23,016 VariantAnnotator - Processed 5 loci. | |
| [2014-10-03 19:07] | |
| [2014-10-03 19:07] INFO 19:07:23,026 ProgressMeter - done 15.0 1.0 s 23.3 h 80.0% 1.0 s 0.0 s | |
| [2014-10-03 19:07] INFO 19:07:23,028 ProgressMeter - Total runtime 1.26 secs, 0.02 min, 0.00 hours | |
| [2014-10-03 19:07] INFO 19:07:23,029 MicroScheduler - 152 reads were filtered out during the traversal out of approximately 4034 total reads (3.77%) | |
| [2014-10-03 19:07] INFO 19:07:23,029 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 19:07] INFO 19:07:23,030 MicroScheduler - -> 152 reads (3.77% of total) failing DuplicateReadFilter | |
| [2014-10-03 19:07] INFO 19:07:23,030 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter | |
| [2014-10-03 19:07] INFO 19:07:23,031 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 19:07] INFO 19:07:23,031 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 19:07] INFO 19:07:23,032 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter | |
| [2014-10-03 19:07] INFO 19:07:30,490 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 19:07] Genotyping with FreeBayes | |
| [2014-10-03 19:07] tabix index TestBatch1-chr22_0_14496-raw.vcf.gz | |
| [2014-10-03 19:07] GATK: VariantAnnotator | |
| [2014-10-03 19:07] INFO 19:07:32,331 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:32,333 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 19:07] INFO 19:07:32,333 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:07] INFO 19:07:32,334 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:07] INFO 19:07:32,336 HelpFormatter - Program Args: -T VariantAnnotator -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chr22/TestBatch1-chr22_0_14496-raw.vcf.gz --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/tmptest/bcbiotx/85ee0b9c-4b30-11e4-9a0e-080027201064/tmprQmmAc/TestBatch1-chr22_0_14496-raw-gatkann.vcf.gz -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chr22/TestBatch1-chr22_0_14496-raw.vcf.gz --dbsnp /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality -A DepthPerAlleleBySample -A Coverage --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment | |
| [2014-10-03 19:07] INFO 19:07:32,339 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:07] INFO 19:07:32,340 HelpFormatter - Date/Time: 2014/10/03 19:07:32 | |
| [2014-10-03 19:07] INFO 19:07:32,340 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:32,341 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:32,826 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:07] INFO 19:07:32,887 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 | |
| [2014-10-03 19:07] INFO 19:07:32,892 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 19:07] INFO 19:07:32,899 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 19:07] INFO 19:07:32,955 IntervalUtils - Processing 6 bp from intervals | |
| [2014-10-03 19:07] WARN 19:07:32,958 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:07] WARN 19:07:32,962 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:07] INFO 19:07:33,031 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 19:07] INFO 19:07:33,046 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:33,049 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:07] INFO 19:07:33,050 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 19:07] INFO 19:07:33,051 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 19:07] INFO 19:07:33,234 VariantAnnotator - Processed 4 loci. | |
| [2014-10-03 19:07] | |
| [2014-10-03 19:07] INFO 19:07:33,242 ProgressMeter - done 18.0 0.0 s 3.0 h 83.3% 0.0 s 0.0 s | |
| [2014-10-03 19:07] INFO 19:07:33,244 ProgressMeter - Total runtime 0.19 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:07] INFO 19:07:33,245 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 9 total reads (0.00%) | |
| [2014-10-03 19:07] INFO 19:07:33,246 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter | |
| [2014-10-03 19:07] INFO 19:07:33,247 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter | |
| [2014-10-03 19:07] INFO 19:07:33,247 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter | |
| [2014-10-03 19:07] INFO 19:07:33,248 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter | |
| [2014-10-03 19:07] INFO 19:07:33,248 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter | |
| [2014-10-03 19:07] INFO 19:07:33,249 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter | |
| [2014-10-03 19:07] INFO 19:07:39,526 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 19:07] Genotyping with FreeBayes | |
| [2014-10-03 19:07] tabix index TestBatch1-chr22_15128_15500-raw.vcf.gz | |
| [2014-10-03 19:07] GATK: VariantAnnotator | |
| [2014-10-03 19:07] INFO 19:07:41,362 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:41,364 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 | |
| [2014-10-03 19:07] INFO 19:07:41,365 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:07] INFO 19:07:41,366 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:07] INFO 19:07:41,369 HelpFormatter - Program Args: -T VariantAnnotator -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chr22/TestBatch1-chr22_15128_15500-raw.vcf.gz --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/tmptest/bcbiotx/8b50f1f8-4b30-11e4-9a0e-080027201064/tmpPehz8y/TestBatch1-chr22_15128_15500-raw-gatkann.vcf.gz -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chr22/TestBatch1-chr22_15128_15500-raw.vcf.gz --dbsnp /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort.bam -A BaseQualityRankSumTest -A FisherStrand -A GCContent -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality -A DepthPerAlleleBySample -A Coverage --allow_potentially_misencoded_quality_scores -U ALL --read_filter BadCigar --read_filter NotPrimaryAlignment | |
| [2014-10-03 19:07] INFO 19:07:41,371 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:07] INFO 19:07:41,372 HelpFormatter - Date/Time: 2014/10/03 19:07:41 | |
| [2014-10-03 19:07] INFO 19:07:41,373 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:41,373 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:41,879 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:07] INFO 19:07:41,940 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 | |
| [2014-10-03 19:07] INFO 19:07:41,946 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 19:07] INFO 19:07:41,955 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 | |
| [2014-10-03 19:07] WARN 19:07:42,005 IntervalUtils - The interval file /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/chr22/TestBatch1-chr22_15128_15500-raw.vcf.gz contains no intervals that could be parsed. | |
| [2014-10-03 19:07] INFO 19:07:42,007 IntervalUtils - Processing 0 bp from intervals | |
| [2014-10-03 19:07] WARN 19:07:42,008 GenomeAnalysisEngine - The given combination of -L and -XL options results in an empty set. No intervals to process. | |
| [2014-10-03 19:07] WARN 19:07:42,016 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:07] WARN 19:07:42,017 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:07] INFO 19:07:42,082 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 19:07] INFO 19:07:42,084 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:42,085 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:07] INFO 19:07:42,086 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 19:07] INFO 19:07:42,089 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 19:07] INFO 19:07:42,153 VariantAnnotator - Processed 0 loci. | |
| [2014-10-03 19:07] | |
| [2014-10-03 19:07] INFO 19:07:42,165 ProgressMeter - done 0.0 0.0 s 22.0 h 0.0% 0.0 s 0.0 s | |
| [2014-10-03 19:07] INFO 19:07:42,166 ProgressMeter - Total runtime 0.08 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:07] INFO 19:07:48,506 GATKRunReport - Uploaded run statistics report to AWS S3 | |
| [2014-10-03 19:07] multiprocessing: concat_variant_files | |
| [2014-10-03 19:07] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:07] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:07] Concat variant files | |
| [2014-10-03 19:07] INFO 19:07:49,808 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:49,814 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants | |
| [2014-10-03 19:07] INFO 19:07:49,817 HelpFormatter - Program Args: -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -V /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/TestBatch1-files.list -out /home/vagrant/bcbio-nextgen/tests/test_automated_output/tmptest/bcbiotx/90a4ff0a-4b30-11e4-9a0e-080027201064/tmpqPimUP/TestBatch1.vcf.gz -assumeSorted | |
| [2014-10-03 19:07] INFO 19:07:49,819 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:07] INFO 19:07:49,823 HelpFormatter - Date/Time: 2014/10/03 19:07:49 | |
| [2014-10-03 19:07] INFO 19:07:49,823 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:49,824 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 19:07] .... | |
| [2014-10-03 19:07] Resource requests: bamtools, bcbio_variation, fastqc, gatk, gemini, qsignature, samtools, snpeff; memory: 2.5, 3.5, 2.0, 2.0, 6.0; cores: 1, 1, 1, 1, 16, 1, 16, 1 | |
| [2014-10-03 19:07] Configuring 1 jobs to run, using 1 cores each with 6.2g of memory reserved for each job | |
| [2014-10-03 19:07] Timing: joint squaring off/backfilling | |
| [2014-10-03 19:07] Timing: variant post-processing | |
| [2014-10-03 19:07] multiprocessing: postprocess_variants | |
| [2014-10-03 19:07] Finalizing variant calls: VarOnly, None | |
| [2014-10-03 19:07] Finalizing variant calls: Test1, freebayes | |
| [2014-10-03 19:07] Calculating variation effects for Test1, freebayes | |
| [2014-10-03 19:07] snpEff effects : Test1 | |
| [2014-10-03 19:07] | |
| [2014-10-03 19:07] WARNINGS: Some warning were detected | |
| [2014-10-03 19:07] Warning type Number of warnings | |
| [2014-10-03 19:07] WARNING_TRANSCRIPT_INCOMPLETE 19 | |
| [2014-10-03 19:07] WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS 9 | |
| [2014-10-03 19:07] | |
| [2014-10-03 19:07] | |
| [2014-10-03 19:07] tabix index TestBatch1-effects.vcf.gz | |
| [2014-10-03 19:07] Filtering for Test1, freebayes | |
| [2014-10-03 19:07] bgzip TestBatch1-effects-ploidyfix.vcf | |
| [2014-10-03 19:07] tabix index TestBatch1-effects-ploidyfix.vcf.gz | |
| [2014-10-03 19:07] Hard filtering /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/TestBatch1-effects-ploidyfix.vcf.gz with (AF[0] <= 0.5 && (DP < 4 || (DP < 13 && %QUAL < 10))) || (AF[0] > 0.5 && (DP < 4 && %QUAL < 50)) || (%QUAL < 424.0 && DP > 212 && AF[0] <= 0.5) : Test1 | |
| [2014-10-03 19:07] tabix index TestBatch1-effects-ploidyfix-filter.vcf.gz | |
| [2014-10-03 19:07] multiprocessing: split_variants_by_sample | |
| [2014-10-03 19:07] Timing: prepped BAM merging | |
| [2014-10-03 19:07] Timing: validation | |
| [2014-10-03 19:07] multiprocessing: compare_to_rm | |
| [2014-10-03 19:07] Comparing variant calls using bcbio.variation : VarOnly | |
| [2014-10-03 19:07] 2014-10-03 19:07:53,929 [INFO ] MLog clients using log4j logging. | |
| [2014-10-03 19:07] 2014-10-03 19:07:54,177 [INFO ] State :begin :: {:desc "Starting variation analysis"} | |
| [2014-10-03 19:07] 2014-10-03 19:07:54,202 [INFO ] State :clean :: {:desc "Cleaning input VCF: ref"} | |
| [2014-10-03 19:07] 2014-10-03 19:07:54,402 [INFO ] State :merge :: {:desc "Merging multiple input files: ref"} | |
| [2014-10-03 19:07] 2014-10-03 19:07:54,408 [INFO ] State :prep :: {:desc "Prepare VCF, resorting to genome build: ref"} | |
| [2014-10-03 19:07] INFO 19:07:57,246 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:57,247 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:07] INFO 19:07:57,248 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:07] INFO 19:07:57,248 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:07] INFO 19:07:57,251 HelpFormatter - Program Args: -T SelectVariants --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name VarOnly --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/prep/VarOnly-ref-prep.vcf --unsafe ALL --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/prep/txtmp3950259931727222497/VarOnly-ref-noref.vcf --excludeNonVariants --excludeFiltered -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:07] INFO 19:07:57,254 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:07] INFO 19:07:57,254 HelpFormatter - Date/Time: 2014/10/03 19:07:57 | |
| [2014-10-03 19:07] INFO 19:07:57,256 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:57,256 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:57,812 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:07] INFO 19:07:57,880 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:07] INFO 19:07:57,896 IntervalUtils - Processing 5150 bp from intervals | |
| [2014-10-03 19:07] INFO 19:07:57,933 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:57,935 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:57,935 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:07] INFO 19:07:57,936 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:07] INFO 19:07:57,939 SelectVariants - Including sample 'VarOnly' | |
| [2014-10-03 19:07] INFO 19:07:57,996 SelectVariants - 9 records processed. | |
| [2014-10-03 19:07] INFO 19:07:57,998 ProgressMeter - done 9.00e+00 0.0 s 115.4 m 22.5% 0.0 s 0.0 s | |
| [2014-10-03 19:07] INFO 19:07:57,999 ProgressMeter - Total runtime 0.06 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:07] INFO 19:07:58,091 NativeMethodAccessorImpl - State :normalize :: {:desc "Normalize MNP and indel variants: ref"} | |
| [2014-10-03 19:07] INFO 19:07:58,157 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:58,158 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:07] INFO 19:07:58,158 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:07] INFO 19:07:58,159 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:07] INFO 19:07:58,159 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/prep/txtmp7909935755216117205/VarOnly-ref-noref-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/prep/VarOnly-ref-noref.vcf | |
| [2014-10-03 19:07] INFO 19:07:58,160 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:07] INFO 19:07:58,160 HelpFormatter - Date/Time: 2014/10/03 19:07:58 | |
| [2014-10-03 19:07] INFO 19:07:58,161 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:58,162 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:58,166 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:07] INFO 19:07:58,188 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:07] INFO 19:07:58,193 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:58,194 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:58,195 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:07] INFO 19:07:58,195 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:07] 0 variants were aligned | |
| [2014-10-03 19:07] INFO 19:07:58,246 ProgressMeter - done 9.00e+00 0.0 s 93.8 m 0.4% 0.0 s 0.0 s | |
| [2014-10-03 19:07] INFO 19:07:58,246 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:07] INFO 19:07:58,416 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:58,419 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:07] INFO 19:07:58,420 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:07] INFO 19:07:58,421 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:07] INFO 19:07:58,421 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/prep/txtmp101510170808443770/VarOnly-ref-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/prep/VarOnly-ref-worknomnp.vcf | |
| [2014-10-03 19:07] INFO 19:07:58,427 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:07] INFO 19:07:58,427 HelpFormatter - Date/Time: 2014/10/03 19:07:58 | |
| [2014-10-03 19:07] INFO 19:07:58,428 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:58,428 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:58,432 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:07] INFO 19:07:58,453 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:07] INFO 19:07:58,457 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:58,458 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:58,459 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:07] INFO 19:07:58,459 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:07] 0 variants were aligned | |
| [2014-10-03 19:07] INFO 19:07:58,475 ProgressMeter - done 9.00e+00 0.0 s 28.8 m 0.4% 0.0 s 0.0 s | |
| [2014-10-03 19:07] INFO 19:07:58,476 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:07] INFO 19:07:58,539 NativeMethodAccessorImpl - State :clean :: {:desc "Cleaning input VCF: eval"} | |
| [2014-10-03 19:07] INFO 19:07:58,540 NativeMethodAccessorImpl - State :merge :: {:desc "Merging multiple input files: eval"} | |
| [2014-10-03 19:07] INFO 19:07:58,541 NativeMethodAccessorImpl - State :prep :: {:desc "Prepare VCF, resorting to genome build: eval"} | |
| [2014-10-03 19:07] INFO 19:07:58,620 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:58,621 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:07] INFO 19:07:58,621 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:07] INFO 19:07:58,622 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:07] INFO 19:07:58,622 HelpFormatter - Program Args: -T SelectVariants --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name GradeRM --variant /home/vagrant/bcbio-nextgen/tests/data/reference_material/7_100326_FC6107FAAXX-grade.vcf --unsafe ALL --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/prep/txtmp3110280985572833527/VarOnly-eval-noref.vcf --excludeNonVariants --excludeFiltered -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:07] INFO 19:07:58,623 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:07] INFO 19:07:58,623 HelpFormatter - Date/Time: 2014/10/03 19:07:58 | |
| [2014-10-03 19:07] INFO 19:07:58,624 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:58,624 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:58,644 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:07] INFO 19:07:58,661 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:07] INFO 19:07:58,666 IntervalUtils - Processing 5150 bp from intervals | |
| [2014-10-03 19:07] INFO 19:07:58,667 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:58,668 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:58,669 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:07] INFO 19:07:58,669 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:07] INFO 19:07:58,670 SelectVariants - Including sample 'GradeRM' | |
| [2014-10-03 19:07] INFO 19:07:58,694 SelectVariants - 9 records processed. | |
| [2014-10-03 19:07] INFO 19:07:58,696 ProgressMeter - done 9.00e+00 0.0 s 50.6 m 22.5% 0.0 s 0.0 s | |
| [2014-10-03 19:07] INFO 19:07:58,697 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:07] INFO 19:07:58,759 NativeMethodAccessorImpl - State :normalize :: {:desc "Normalize MNP and indel variants: eval"} | |
| [2014-10-03 19:07] INFO 19:07:58,788 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:58,789 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:07] INFO 19:07:58,789 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:07] INFO 19:07:58,790 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:07] INFO 19:07:58,791 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/prep/txtmp5959871911478777182/VarOnly-eval-noref-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/prep/VarOnly-eval-noref.vcf | |
| [2014-10-03 19:07] INFO 19:07:58,792 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:07] INFO 19:07:58,792 HelpFormatter - Date/Time: 2014/10/03 19:07:58 | |
| [2014-10-03 19:07] INFO 19:07:58,793 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:58,793 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:58,800 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:07] INFO 19:07:58,812 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:07] INFO 19:07:58,815 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:58,815 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:58,815 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:07] INFO 19:07:58,817 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:07] 0 variants were aligned | |
| [2014-10-03 19:07] INFO 19:07:58,835 ProgressMeter - done 9.00e+00 0.0 s 37.1 m 0.4% 0.0 s 0.0 s | |
| [2014-10-03 19:07] INFO 19:07:58,835 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:07] INFO 19:07:58,944 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:58,950 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:07] INFO 19:07:58,951 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:07] INFO 19:07:58,952 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:07] INFO 19:07:58,952 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/prep/txtmp3962290592468009375/VarOnly-eval-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/prep/VarOnly-eval-worknomnp.vcf | |
| [2014-10-03 19:07] INFO 19:07:58,953 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:07] INFO 19:07:58,953 HelpFormatter - Date/Time: 2014/10/03 19:07:58 | |
| [2014-10-03 19:07] INFO 19:07:58,954 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:58,954 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:58,961 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:07] INFO 19:07:58,994 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:07] INFO 19:07:58,996 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:58,996 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:58,996 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:07] INFO 19:07:58,996 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:07] 0 variants were aligned | |
| [2014-10-03 19:07] INFO 19:07:59,010 ProgressMeter - done 9.00e+00 0.0 s 25.1 m 0.4% 0.0 s 0.0 s | |
| [2014-10-03 19:07] INFO 19:07:59,011 ProgressMeter - Total runtime 0.01 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:07] INFO 19:07:59,081 NativeMethodAccessorImpl - State :combine :: {:desc "Creating merged VCF files for all comparisons"} | |
| [2014-10-03 19:07] INFO 19:07:59,083 NativeMethodAccessorImpl - State :annotate :: {:desc "Annotate VCFs with metrics"} | |
| [2014-10-03 19:07] INFO 19:07:59,084 NativeMethodAccessorImpl - State :filter :: {:desc "Post annotation filtering"} | |
| [2014-10-03 19:07] INFO 19:07:59,086 NativeMethodAccessorImpl - State :compare :: {:desc "Comparing VCFs: ref vs eval"} | |
| [2014-10-03 19:07] INFO 19:07:59,214 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:59,214 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:07] INFO 19:07:59,215 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:07] INFO 19:07:59,215 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:07] INFO 19:07:59,216 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name VarOnly --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/prep/VarOnly-eval-nomnp-nosv.vcf --concordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/prep/VarOnly-ref-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/txtmp2990611797298562480/VarOnly-eval-ref-concordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:07] INFO 19:07:59,217 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:07] INFO 19:07:59,217 HelpFormatter - Date/Time: 2014/10/03 19:07:59 | |
| [2014-10-03 19:07] INFO 19:07:59,218 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:59,218 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:59,229 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:07] INFO 19:07:59,241 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:07] INFO 19:07:59,253 IntervalUtils - Processing 5150 bp from intervals | |
| [2014-10-03 19:07] INFO 19:07:59,254 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:59,255 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:59,255 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:07] INFO 19:07:59,256 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:07] INFO 19:07:59,256 SelectVariants - Including sample 'VarOnly' | |
| [2014-10-03 19:07] INFO 19:07:59,257 SelectVariants - Selecting only variants concordant with the track: concordance | |
| [2014-10-03 19:07] INFO 19:07:59,282 SelectVariants - 9 records processed. | |
| [2014-10-03 19:07] INFO 19:07:59,288 ProgressMeter - done 9.00e+00 0.0 s 61.0 m 22.5% 0.0 s 0.0 s | |
| [2014-10-03 19:07] INFO 19:07:59,289 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:07] INFO 19:07:59,414 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:59,416 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:07] INFO 19:07:59,416 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:07] INFO 19:07:59,417 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:07] INFO 19:07:59,417 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name VarOnly --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/prep/VarOnly-ref-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/prep/VarOnly-eval-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/txtmp910037843108248493/VarOnly-ref-eval-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:07] INFO 19:07:59,418 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:07] INFO 19:07:59,419 HelpFormatter - Date/Time: 2014/10/03 19:07:59 | |
| [2014-10-03 19:07] INFO 19:07:59,419 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:59,419 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:59,428 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:07] INFO 19:07:59,439 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:07] INFO 19:07:59,445 IntervalUtils - Processing 5150 bp from intervals | |
| [2014-10-03 19:07] INFO 19:07:59,446 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:59,447 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:59,447 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:07] INFO 19:07:59,448 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:07] INFO 19:07:59,448 SelectVariants - Including sample 'VarOnly' | |
| [2014-10-03 19:07] INFO 19:07:59,449 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:07] INFO 19:07:59,465 SelectVariants - 9 records processed. | |
| [2014-10-03 19:07] INFO 19:07:59,466 ProgressMeter - done 9.00e+00 0.0 s 34.6 m 22.5% 0.0 s 0.0 s | |
| [2014-10-03 19:07] INFO 19:07:59,467 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:07] INFO 19:07:59,552 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:59,553 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:07] INFO 19:07:59,554 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:07] INFO 19:07:59,554 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:07] INFO 19:07:59,555 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name VarOnly --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/prep/VarOnly-eval-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/prep/VarOnly-ref-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/txtmp6900564131972640708/VarOnly-eval-ref-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:07] INFO 19:07:59,555 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:07] INFO 19:07:59,556 HelpFormatter - Date/Time: 2014/10/03 19:07:59 | |
| [2014-10-03 19:07] INFO 19:07:59,557 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:59,557 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:59,563 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:07] INFO 19:07:59,575 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:07] INFO 19:07:59,581 IntervalUtils - Processing 5150 bp from intervals | |
| [2014-10-03 19:07] INFO 19:07:59,587 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:59,587 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:59,588 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:07] INFO 19:07:59,589 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:07] INFO 19:07:59,590 SelectVariants - Including sample 'VarOnly' | |
| [2014-10-03 19:07] INFO 19:07:59,593 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:07] INFO 19:07:59,615 SelectVariants - 9 records processed. | |
| [2014-10-03 19:07] INFO 19:07:59,616 ProgressMeter - done 9.00e+00 0.0 s 51.3 m 22.5% 0.0 s 0.0 s | |
| [2014-10-03 19:07] INFO 19:07:59,619 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:07] INFO 19:07:59,717 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:59,718 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:07] INFO 19:07:59,718 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:07] INFO 19:07:59,719 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:07] INFO 19:07:59,719 HelpFormatter - Program Args: -T CombineVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/txtmp5316782109772315592/VarOnly-eval-ref-discordance-fullcombine.vcf --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null --variant:v0 /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/VarOnly-eval-ref-discordance.vcf --variant:v1 /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/work/VarOnly-ref-eval-discordance-asref.vcf --genotypemergeoption PRIORITIZE | |
| [2014-10-03 19:07] INFO 19:07:59,720 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:07] INFO 19:07:59,720 HelpFormatter - Date/Time: 2014/10/03 19:07:59 | |
| [2014-10-03 19:07] INFO 19:07:59,721 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:59,721 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:07] INFO 19:07:59,730 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:07] INFO 19:07:59,749 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:07] INFO 19:07:59,755 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:59,756 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:07] INFO 19:07:59,756 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:07] INFO 19:07:59,756 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:07] INFO 19:07:59,759 ProgressMeter - done 0.00e+00 0.0 s 52.9 m 100.0% 0.0 s 0.0 s | |
| [2014-10-03 19:07] INFO 19:07:59,762 ProgressMeter - Total runtime 0.01 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:07] INFO 19:07:59,839 NativeMethodAccessorImpl - State :summary :: {:desc "Summarize comparisons"} | |
| [2014-10-03 19:08] INFO 19:08:00,849 C3P0Registry - Initializing c3p0-0.9.1.2 [built 21-May-2007 15:04:56; debug? true; trace: 10] | |
| [2014-10-03 19:08] INFO 19:08:00,960 NativeMethodAccessorImpl - State :finished :: {:desc "Finished"} | |
| [2014-10-03 19:08] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:08] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:08] Comparing variant calls using bcbio.variation : Test1 | |
| [2014-10-03 19:08] 2014-10-03 19:08:03,859 [INFO ] MLog clients using log4j logging. | |
| [2014-10-03 19:08] 2014-10-03 19:08:04,106 [INFO ] State :begin :: {:desc "Starting variation analysis"} | |
| [2014-10-03 19:08] 2014-10-03 19:08:04,136 [INFO ] State :clean :: {:desc "Cleaning input VCF: ref"} | |
| [2014-10-03 19:08] 2014-10-03 19:08:04,333 [INFO ] State :merge :: {:desc "Merging multiple input files: ref"} | |
| [2014-10-03 19:08] 2014-10-03 19:08:04,340 [INFO ] State :prep :: {:desc "Prepare VCF, resorting to genome build: ref"} | |
| [2014-10-03 19:08] INFO 19:08:07,211 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:07,213 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:08] INFO 19:08:07,214 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:08] INFO 19:08:07,214 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:08] INFO 19:08:07,217 HelpFormatter - Program Args: -T SelectVariants --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-ref-prep.vcf --unsafe ALL --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/txtmp8507944078221768209/Test1-ref-noref.vcf --excludeNonVariants --excludeFiltered -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:08] INFO 19:08:07,219 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:08] INFO 19:08:07,220 HelpFormatter - Date/Time: 2014/10/03 19:08:07 | |
| [2014-10-03 19:08] INFO 19:08:07,221 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:07,222 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:07,777 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:08] INFO 19:08:07,839 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:08] INFO 19:08:07,856 IntervalUtils - Processing 4426 bp from intervals | |
| [2014-10-03 19:08] INFO 19:08:07,892 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:07,893 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:07,894 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:08] INFO 19:08:07,895 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:08] INFO 19:08:07,898 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:08] INFO 19:08:07,966 SelectVariants - 9 records processed. | |
| [2014-10-03 19:08] INFO 19:08:07,968 ProgressMeter - done 9.00e+00 0.0 s 2.3 h 26.2% 0.0 s 0.0 s | |
| [2014-10-03 19:08] INFO 19:08:07,969 ProgressMeter - Total runtime 0.08 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:08] INFO 19:08:08,055 NativeMethodAccessorImpl - State :normalize :: {:desc "Normalize MNP and indel variants: ref"} | |
| [2014-10-03 19:08] INFO 19:08:08,111 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:08,112 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:08] INFO 19:08:08,113 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:08] INFO 19:08:08,113 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:08] INFO 19:08:08,114 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/txtmp2836802363440425302/Test1-ref-noref-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-ref-noref.vcf | |
| [2014-10-03 19:08] INFO 19:08:08,115 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:08] INFO 19:08:08,115 HelpFormatter - Date/Time: 2014/10/03 19:08:08 | |
| [2014-10-03 19:08] INFO 19:08:08,116 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:08,116 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:08,123 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:08] INFO 19:08:08,144 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:08] INFO 19:08:08,152 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:08,153 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:08,154 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:08] INFO 19:08:08,154 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:08] 0 variants were aligned | |
| [2014-10-03 19:08] INFO 19:08:08,201 ProgressMeter - done 9.00e+00 0.0 s 86.9 m 0.4% 0.0 s 0.0 s | |
| [2014-10-03 19:08] INFO 19:08:08,202 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:08] INFO 19:08:08,371 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:08,374 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:08] INFO 19:08:08,375 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:08] INFO 19:08:08,375 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:08] INFO 19:08:08,376 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/txtmp2192116527116705533/Test1-ref-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-ref-worknomnp.vcf | |
| [2014-10-03 19:08] INFO 19:08:08,376 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:08] INFO 19:08:08,377 HelpFormatter - Date/Time: 2014/10/03 19:08:08 | |
| [2014-10-03 19:08] INFO 19:08:08,377 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:08,378 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:08,385 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:08] INFO 19:08:08,410 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:08] INFO 19:08:08,413 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:08,414 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:08,414 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:08] INFO 19:08:08,415 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:08] 0 variants were aligned | |
| [2014-10-03 19:08] INFO 19:08:08,432 ProgressMeter - done 9.00e+00 0.0 s 32.1 m 0.4% 0.0 s 0.0 s | |
| [2014-10-03 19:08] INFO 19:08:08,433 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:08] INFO 19:08:08,496 NativeMethodAccessorImpl - State :clean :: {:desc "Cleaning input VCF: eval"} | |
| [2014-10-03 19:08] INFO 19:08:08,497 NativeMethodAccessorImpl - State :merge :: {:desc "Merging multiple input files: eval"} | |
| [2014-10-03 19:08] INFO 19:08:08,498 NativeMethodAccessorImpl - State :prep :: {:desc "Prepare VCF, resorting to genome build: eval"} | |
| [2014-10-03 19:08] INFO 19:08:08,578 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:08,579 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:08] INFO 19:08:08,580 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:08] INFO 19:08:08,580 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:08] INFO 19:08:08,581 HelpFormatter - Program Args: -T SelectVariants --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/freebayes/Test1-effects-ploidyfix-filter.vcf.gz --unsafe ALL --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/txtmp6873632569668109959/Test1-eval-noref.vcf --excludeNonVariants --excludeFiltered -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:08] INFO 19:08:08,581 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:08] INFO 19:08:08,582 HelpFormatter - Date/Time: 2014/10/03 19:08:08 | |
| [2014-10-03 19:08] INFO 19:08:08,583 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:08,583 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:08,603 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:08] INFO 19:08:08,621 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:08] INFO 19:08:08,625 IntervalUtils - Processing 4426 bp from intervals | |
| [2014-10-03 19:08] WARN 19:08:08,626 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:08] INFO 19:08:08,627 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:08,627 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:08,628 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:08] INFO 19:08:08,628 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:08] INFO 19:08:08,629 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:08] INFO 19:08:08,712 SelectVariants - 10 records processed. | |
| [2014-10-03 19:08] INFO 19:08:08,714 ProgressMeter - done 1.00e+01 0.0 s 2.4 h 90.1% 0.0 s 0.0 s | |
| [2014-10-03 19:08] INFO 19:08:08,715 ProgressMeter - Total runtime 0.09 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:08] INFO 19:08:08,803 NativeMethodAccessorImpl - State :normalize :: {:desc "Normalize MNP and indel variants: eval"} | |
| [2014-10-03 19:08] INFO 19:08:08,836 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:08,837 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:08] INFO 19:08:08,837 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:08] INFO 19:08:08,837 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:08] INFO 19:08:08,838 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/txtmp2938387699409457452/Test1-eval-noref-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-eval-noref.vcf | |
| [2014-10-03 19:08] INFO 19:08:08,839 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:08] INFO 19:08:08,839 HelpFormatter - Date/Time: 2014/10/03 19:08:08 | |
| [2014-10-03 19:08] INFO 19:08:08,840 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:08,840 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:08,844 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:08] INFO 19:08:08,856 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:08] INFO 19:08:08,860 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:08,861 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:08,861 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:08] INFO 19:08:08,862 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:08] 0 variants were aligned | |
| [2014-10-03 19:08] INFO 19:08:08,885 ProgressMeter - done 1.00e+01 0.0 s 39.1 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 19:08] INFO 19:08:08,886 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:08] INFO 19:08:09,029 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:09,030 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:08] INFO 19:08:09,031 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:08] INFO 19:08:09,031 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:08] INFO 19:08:09,032 HelpFormatter - Program Args: -T LeftAlignVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/txtmp8323205160426186864/Test1-eval-worknomnp-leftalign.vcf --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-eval-worknomnp.vcf | |
| [2014-10-03 19:08] INFO 19:08:09,035 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:08] INFO 19:08:09,035 HelpFormatter - Date/Time: 2014/10/03 19:08:09 | |
| [2014-10-03 19:08] INFO 19:08:09,036 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:09,036 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:09,048 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:08] INFO 19:08:09,079 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:08] INFO 19:08:09,088 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:09,089 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:09,090 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:08] INFO 19:08:09,090 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:08] 0 variants were aligned | |
| [2014-10-03 19:08] INFO 19:08:09,123 ProgressMeter - done 1.00e+01 0.0 s 54.3 m 84.7% 0.0 s 0.0 s | |
| [2014-10-03 19:08] INFO 19:08:09,124 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:08] INFO 19:08:09,198 NativeMethodAccessorImpl - State :combine :: {:desc "Creating merged VCF files for all comparisons"} | |
| [2014-10-03 19:08] INFO 19:08:09,200 NativeMethodAccessorImpl - State :annotate :: {:desc "Annotate VCFs with metrics"} | |
| [2014-10-03 19:08] INFO 19:08:09,202 NativeMethodAccessorImpl - State :filter :: {:desc "Post annotation filtering"} | |
| [2014-10-03 19:08] INFO 19:08:09,209 NativeMethodAccessorImpl - State :compare :: {:desc "Comparing VCFs: ref vs eval"} | |
| [2014-10-03 19:08] INFO 19:08:09,430 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:09,433 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:08] INFO 19:08:09,433 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:08] INFO 19:08:09,434 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:08] INFO 19:08:09,434 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-eval-nomnp-nosv.vcf --concordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-ref-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/txtmp7907811173188959758/Test1-eval-ref-concordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:08] INFO 19:08:09,435 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:08] INFO 19:08:09,436 HelpFormatter - Date/Time: 2014/10/03 19:08:09 | |
| [2014-10-03 19:08] INFO 19:08:09,436 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:09,437 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:09,450 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:08] INFO 19:08:09,466 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:08] INFO 19:08:09,479 IntervalUtils - Processing 4426 bp from intervals | |
| [2014-10-03 19:08] INFO 19:08:09,479 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:09,480 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:09,481 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:08] INFO 19:08:09,481 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:08] INFO 19:08:09,482 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:08] INFO 19:08:09,486 SelectVariants - Selecting only variants concordant with the track: concordance | |
| [2014-10-03 19:08] INFO 19:08:09,524 SelectVariants - 10 records processed. | |
| [2014-10-03 19:08] INFO 19:08:09,526 ProgressMeter - done 1.00e+01 0.0 s 75.0 m 90.1% 0.0 s 0.0 s | |
| [2014-10-03 19:08] INFO 19:08:09,527 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:08] INFO 19:08:09,652 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:09,653 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:08] INFO 19:08:09,653 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:08] INFO 19:08:09,654 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:08] INFO 19:08:09,654 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-ref-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-eval-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/txtmp5720020437804303605/Test1-ref-eval-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:08] INFO 19:08:09,655 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:08] INFO 19:08:09,655 HelpFormatter - Date/Time: 2014/10/03 19:08:09 | |
| [2014-10-03 19:08] INFO 19:08:09,656 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:09,656 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:09,663 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:08] INFO 19:08:09,674 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:08] INFO 19:08:09,681 IntervalUtils - Processing 4426 bp from intervals | |
| [2014-10-03 19:08] INFO 19:08:09,682 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:09,684 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:09,684 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:08] INFO 19:08:09,685 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:08] INFO 19:08:09,685 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:08] INFO 19:08:09,686 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:08] INFO 19:08:09,702 SelectVariants - 9 records processed. | |
| [2014-10-03 19:08] INFO 19:08:09,704 ProgressMeter - done 1.00e+01 0.0 s 31.7 m 90.1% 0.0 s 0.0 s | |
| [2014-10-03 19:08] INFO 19:08:09,704 ProgressMeter - Total runtime 0.02 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:08] INFO 19:08:09,792 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:09,793 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:08] INFO 19:08:09,794 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:08] INFO 19:08:09,794 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:08] INFO 19:08:09,795 HelpFormatter - Program Args: -T SelectVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --sample_name Test1 --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-eval-nomnp-nosv.vcf --discordance /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/prep/Test1-ref-nomnp-nosv.vcf --out /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/txtmp6061472207541379727/Test1-eval-ref-discordance.vcf -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-callable_sample-sorted.bed --interval_set_rule INTERSECTION | |
| [2014-10-03 19:08] INFO 19:08:09,795 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:08] INFO 19:08:09,796 HelpFormatter - Date/Time: 2014/10/03 19:08:09 | |
| [2014-10-03 19:08] INFO 19:08:09,796 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:09,797 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:09,803 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:08] INFO 19:08:09,815 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:08] INFO 19:08:09,822 IntervalUtils - Processing 4426 bp from intervals | |
| [2014-10-03 19:08] INFO 19:08:09,823 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:09,824 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:09,824 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:08] INFO 19:08:09,825 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:08] INFO 19:08:09,825 SelectVariants - Including sample 'Test1' | |
| [2014-10-03 19:08] INFO 19:08:09,826 SelectVariants - Selecting only variants discordant with the track: discordance | |
| [2014-10-03 19:08] INFO 19:08:09,850 SelectVariants - 10 records processed. | |
| [2014-10-03 19:08] INFO 19:08:09,852 ProgressMeter - done 1.00e+01 0.0 s 46.2 m 90.1% 0.0 s 0.0 s | |
| [2014-10-03 19:08] INFO 19:08:09,853 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:08] INFO 19:08:09,948 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:09,949 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:08] INFO 19:08:09,950 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:08] INFO 19:08:09,950 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:08] INFO 19:08:09,951 HelpFormatter - Program Args: -T VariantAnnotator --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -I /home/vagrant/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort.bam --variant /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/Test1-ref-eval-discordance-asref.vcf --allow_potentially_misencoded_quality_scores -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/txtmp9102940426554471245/Test1-ref-eval-discordance-asref-annotated.vcf -A DepthOfCoverage -L /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/Test1-ref-eval-discordance-asref.vcf | |
| [2014-10-03 19:08] INFO 19:08:09,951 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:08] INFO 19:08:09,952 HelpFormatter - Date/Time: 2014/10/03 19:08:09 | |
| [2014-10-03 19:08] INFO 19:08:09,952 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:09,953 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:09,966 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:08] INFO 19:08:10,000 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 | |
| [2014-10-03 19:08] INFO 19:08:10,006 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |
| [2014-10-03 19:08] INFO 19:08:10,007 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.00 | |
| [2014-10-03 19:08] WARN 19:08:10,014 IntervalUtils - The interval file /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/Test1-ref-eval-discordance-asref.vcf contains no intervals that could be parsed. | |
| [2014-10-03 19:08] INFO 19:08:10,016 IntervalUtils - Processing 0 bp from intervals | |
| [2014-10-03 19:08] WARN 19:08:10,016 GenomeAnalysisEngine - The given combination of -L and -XL options results in an empty set. No intervals to process. | |
| [2014-10-03 19:08] INFO 19:08:10,017 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files | |
| [2014-10-03 19:08] INFO 19:08:10,023 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:10,024 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:08] INFO 19:08:10,024 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:08] INFO 19:08:10,052 VariantAnnotator - Processed 0 loci. | |
| [2014-10-03 19:08] | |
| [2014-10-03 19:08] INFO 19:08:10,054 ProgressMeter - done 0.00e+00 0.0 s 8.3 h 0.0% 0.0 s 0.0 s | |
| [2014-10-03 19:08] INFO 19:08:10,058 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:08] INFO 19:08:10,159 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:10,160 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.0-6-g9909b24, Compiled 2014/03/08 10:08:34 | |
| [2014-10-03 19:08] INFO 19:08:10,161 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:08] INFO 19:08:10,161 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:08] INFO 19:08:10,162 HelpFormatter - Program Args: -T CombineVariants --unsafe LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/txtmp4408781085857093261/Test1-eval-ref-discordance-fullcombine.vcf --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null --variant:v0 /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/Test1-eval-ref-discordance.vcf --variant:v1 /home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/Test1-ref-eval-discordance-asref-annotated.vcf --genotypemergeoption PRIORITIZE | |
| [2014-10-03 19:08] INFO 19:08:10,162 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:08] INFO 19:08:10,163 HelpFormatter - Date/Time: 2014/10/03 19:08:10 | |
| [2014-10-03 19:08] INFO 19:08:10,163 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:10,164 HelpFormatter - -------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] INFO 19:08:10,170 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:08] INFO 19:08:10,182 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:08] INFO 19:08:10,190 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:10,191 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:08] INFO 19:08:10,191 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:08] INFO 19:08:10,191 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |
| [2014-10-03 19:08] INFO 19:08:10,201 ProgressMeter - done 1.00e+00 0.0 s 2.6 h 84.7% 0.0 s 0.0 s | |
| [2014-10-03 19:08] INFO 19:08:10,202 ProgressMeter - Total runtime 0.01 secs, 0.00 min, 0.00 hours | |
| [2014-10-03 19:08] INFO 19:08:10,278 NativeMethodAccessorImpl - State :summary :: {:desc "Summarize comparisons"} | |
| [2014-10-03 19:08] INFO 19:08:11,255 C3P0Registry - Initializing c3p0-0.9.1.2 [built 21-May-2007 15:04:56; debug? true; trace: 10] | |
| [2014-10-03 19:08] INFO 19:08:11,347 AbstractPoolBackedDataSource - Initializing c3p0 pool... com.mchange.v2.c3p0.ComboPooledDataSource [ acquireIncrement -> 3, acquireRetryAttempts -> 30, acquireRetryDelay -> 1000, autoCommitOnClose -> false, automaticTestTable -> null, breakAfterAcquireFailure -> false, checkoutTimeout -> 0, connectionCustomizerClassName -> null, connectionTesterClassName -> com.mchange.v2.c3p0.impl.DefaultConnectionTester, dataSourceName -> 2rvy8f941nroy9f7s6dic|4573634c, debugUnreturnedConnectionStackTraces -> false, description -> null, driverClass -> org.sqlite.JDBC, factoryClassLocation -> null, forceIgnoreUnresolvedTransactions -> false, identityToken -> 2rvy8f941nroy9f7s6dic|4573634c, idleConnectionTestPeriod -> 0, initialPoolSize -> 3, jdbcUrl -> jdbc:sqlite:/home/vagrant/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/work/Test1-eval-ref-discordance-annotate-gemini.db, maxAdministrativeTaskTime -> 0, maxConnectionAge -> 0, maxIdleTime -> 0, maxIdleTimeExcessConnections -> 0, maxPoolSize -> 15, maxStatements -> 0, maxStatementsPerConnection -> 0, minPoolSize -> 3, numHelperThreads -> 3, numThreadsAwaitingCheckoutDefaultUser -> 0, preferredTestQuery -> null, properties -> {}, propertyCycle -> 0, testConnectionOnCheckin -> false, testConnectionOnCheckout -> false, unreturnedConnectionTimeout -> 0, usesTraditionalReflectiveProxies -> false ] | |
| [2014-10-03 19:08] INFO 19:08:11,623 NativeMethodAccessorImpl - State :finished :: {:desc "Finished"} | |
| [2014-10-03 19:08] Timing: ensemble calling | |
| [2014-10-03 19:08] Timing: validation summary | |
| /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/pandas/core/frame.py:1706: UserWarning: Boolean Series key will be reindexed to match DataFrame index. | |
| "DataFrame index.", UserWarning) | |
| [2014-10-03 19:08] Timing: structural variation | |
| [2014-10-03 19:08] Timing: population database | |
| [2014-10-03 19:08] multiprocessing: prep_gemini_db | |
| [2014-10-03 19:08] Timing: quality control | |
| [2014-10-03 19:08] multiprocessing: pipeline_summary | |
| [2014-10-03 19:08] Generating summary files: ['', 'Test1'] | |
| [2014-10-03 19:08] FastQC: Test1 | |
| [2014-10-03 19:08] Started analysis of Test1-sort.bam | |
| [2014-10-03 19:08] Approx 5% complete for Test1-sort.bam | |
| [2014-10-03 19:08] Approx 10% complete for Test1-sort.bam | |
| [2014-10-03 19:08] Approx 15% complete for Test1-sort.bam | |
| [2014-10-03 19:08] Approx 20% complete for Test1-sort.bam | |
| [2014-10-03 19:08] Approx 25% complete for Test1-sort.bam | |
| [2014-10-03 19:08] Approx 30% complete for Test1-sort.bam | |
| [2014-10-03 19:08] Approx 35% complete for Test1-sort.bam | |
| [2014-10-03 19:08] Approx 40% complete for Test1-sort.bam | |
| [2014-10-03 19:08] Approx 45% complete for Test1-sort.bam | |
| [2014-10-03 19:08] Approx 50% complete for Test1-sort.bam | |
| [2014-10-03 19:08] Approx 55% complete for Test1-sort.bam | |
| [2014-10-03 19:08] Approx 60% complete for Test1-sort.bam | |
| [2014-10-03 19:08] Approx 65% complete for Test1-sort.bam | |
| [2014-10-03 19:08] Approx 70% complete for Test1-sort.bam | |
| [2014-10-03 19:08] Approx 75% complete for Test1-sort.bam | |
| [2014-10-03 19:08] Approx 80% complete for Test1-sort.bam | |
| [2014-10-03 19:08] Approx 85% complete for Test1-sort.bam | |
| [2014-10-03 19:08] Approx 90% complete for Test1-sort.bam | |
| [2014-10-03 19:08] Approx 95% complete for Test1-sort.bam | |
| [2014-10-03 19:08] Approx 100% complete for Test1-sort.bam | |
| [2014-10-03 19:08] Analysis complete for Test1-sort.bam | |
| [2014-10-03 19:08] bamtools stats : Test1 | |
| [2014-10-03 19:08] There is no qsignature for this species: hg19 | |
| [2014-10-03 19:08] multiprocessing: qsignature_summary | |
| [2014-10-03 19:08] Timing: archive | |
| [2014-10-03 19:08] Timing: finished | |
| [2014-10-03 19:08] Storing directory in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/qc | |
| [2014-10-03 19:08] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-ready.bam | |
| [2014-10-03 19:08] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-ready.bam.bai | |
| [2014-10-03 19:08] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-disc.bam | |
| [2014-10-03 19:08] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-disc.bam.bai | |
| [2014-10-03 19:08] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-sr.bam | |
| [2014-10-03 19:08] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-sr.bam.bai | |
| [2014-10-03 19:08] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-freebayes.vcf.gz | |
| [2014-10-03 19:08] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-freebayes.vcf.gz.tbi | |
| [2014-10-03 19:08] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/Test1/Test1-validate.pdf | |
| [2014-10-03 19:08] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/project_2014-10-03/programs.txt | |
| [2014-10-03 19:08] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/project_2014-10-03/bcbio-nextgen.log | |
| [2014-10-03 19:08] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/project_2014-10-03/bcbio-nextgen-commands.log | |
| [2014-10-03 19:08] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/project_2014-10-03/project-summary.yaml | |
| [2014-10-03 19:08] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/project_2014-10-03/TestBatch1-freebayes.vcf.gz | |
| [2014-10-03 19:08] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/project_2014-10-03/TestBatch1-freebayes.vcf.gz.tbi | |
| [2014-10-03 19:08] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/project_2014-10-03/grading-summary.csv | |
| [2014-10-03 19:08] Storing in local filesystem: /home/vagrant/bcbio-nextgen/tests/test_automated_output/upload/project_2014-10-03/bcbio-nextgen.log | |
| ok | |
| Create a project template from input files and metadata configuration. ... variant_regions ../data/100326_FC6107FAAXX/test.bed | |
| sex female | |
| description 7_1 | |
| batch 1a | |
| variant_regions ../data/100326_FC6107FAAXX/test.bed | |
| sex | |
| description 8_1 | |
| batch 1a | |
| Configuration file created at: /home/vagrant/bcbio-nextgen/tests/test_automated_output/100326/config/100326.yaml | |
| Edit to finalize and run with: | |
| cd /home/vagrant/bcbio-nextgen/tests/test_automated_output/100326/work | |
| bcbio_nextgen.py ../config/100326.yaml | |
| ok | |
| Identify programs and versions used in analysis. ... [{'program': 'bcbio-nextgen', 'version': '0.8.3a-9f027b9'}, {'program': 'alientrimmer', 'version': '0.3.2'}, {'program': 'bamtools', 'version': '2.3.0'}, {'program': 'bcbio_variation', 'version': '0.1.7'}, {'program': 'bcftools', 'version': '1.1'}, {'program': 'bedtools', 'version': '2.21.0'}, {'program': 'biobambam', 'version': '0.0.154'}, {'program': 'bowtie2', 'version': '2.2.3'}, {'program': 'bwa', 'version': '0.7.10'}, {'program': 'chanjo', 'version': '2.1.2'}, {'program': 'cn.mops', 'version': '1.10.1'}, {'program': 'cufflinks', 'version': '2.1.1'}, {'program': 'cutadapt', 'version': '1.4.2'}, {'program': 'fastqc', 'version': '0.11.2'}, {'program': 'featurecounts', 'version': '1.4.4'}, {'program': 'freebayes', 'version': '0.9.14-15'}, {'program': 'gatk', 'version': '3.2-2-gec30cee'}, {'program': 'gatk-framework', 'version': '3.2-4'}, {'program': 'gemini', 'version': '0.10.1'}, {'program': 'htseq', 'version': '0.6.1p1'}, {'program': 'mutect', 'version': '1.1.5'}, {'program': 'novoalign', 'version': '3.02.02'}, {'program': 'novosort', 'version': 'V3.00.02'}, {'program': 'oncofuse', 'version': '1.0.7'}, {'program': 'picard', 'version': '1.96'}, {'program': 'platypus-variant', 'version': '0.7.9.2'}, {'program': 'qualimap', 'version': '0.7.1'}, {'program': 'rnaseqc', 'version': '1.1.7'}, {'program': 'sambamba', 'version': '0.4.7'}, {'program': 'samtools', 'version': '1.1'}, {'program': 'snpeff', 'version': '3.6c'}, {'program': 'tophat', 'version': '2.0.9'}, {'program': 'varscan', 'version': '2.3.7'}, {'program': 'vcflib', 'version': '2014-09-29'}, {'program': 'vt', 'version': '2014-09-25'}] | |
| ok | |
| Parallel combination of VCF files, split by chromosome. ... [2014-10-03 19:08] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: bgzip S1-variants.vcf | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bgzip -c /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants.vcf > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpL2dqQO/S1-variants.vcf.gz | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: tabix index S1-variants.vcf.gz | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmphokhNC/S1-variants.vcf.gz | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: bgzip S2-variants.vcf | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bgzip -c /home/vagrant/bcbio-nextgen/tests/data/variants/S2-variants.vcf > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpOiYfVj/S2-variants.vcf.gz | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: tabix index S2-variants.vcf.gz | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpQpXyKh/S2-variants.vcf.gz | |
| [2014-10-03 19:08] INFO: bcbio-nextgen: multiprocessing: merge_variant_files | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: Merge variants | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bcftools merge -O z -r chrM `cat /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/S1_S2-combined-chrM-files.txt` > /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/tx/tmpNLbxUc/S1_S2-combined-chrM.vcf.gz | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: tabix index S1_S2-combined-chrM.vcf.gz | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/tx/tmpIFudw9/S1_S2-combined-chrM.vcf.gz | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: Merge variants | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bcftools merge -O z -r chr22 `cat /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/S1_S2-combined-chr22-files.txt` > /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/tx/tmpXjkdO2/S1_S2-combined-chr22.vcf.gz | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: tabix index S1_S2-combined-chr22.vcf.gz | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/tx/tmp9eS2pn/S1_S2-combined-chr22.vcf.gz | |
| [2014-10-03 19:08] INFO: bcbio-nextgen: multiprocessing: concat_variant_files | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: Concat variant files | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen-commands: /usr/local/bin/gatk-framework org.broadinstitute.gatk.tools.CatVariants -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -V /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-files.list -out /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmprCKlaW/S1_S2-combined.vcf.gz -assumeSorted -Xms500m -Xmx3500m -XX:+UseSerialGC | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:26,029 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:26,032 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:26,034 HelpFormatter - Program Args: -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -V /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-files.list -out /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmprCKlaW/S1_S2-combined.vcf.gz -assumeSorted | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:26,041 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:26,042 HelpFormatter - Date/Time: 2014/10/03 19:08:26 | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:26,043 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:26,043 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: .. | |
| ok | |
| Exclude samples from VCF files. ... [2014-10-03 19:08] DEBUG: bcbio-nextgen: Exclude samples: ['S1'] | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bcftools view -O z -s S2 /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined.vcf.gz > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpDUZh3n/S1_S2-combined-exclude.vcf.gz | |
| ok | |
| Split a VCF file into SNPs and indels, then combine back together. ... [2014-10-03 19:08] DEBUG: bcbio-nextgen: Subset to SNPs and indels | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bcftools view -O v /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants.vcf --types snps > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpS09TuL/S1-variants-snp.vcf | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: Subset to SNPs and indels | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bcftools view -O v /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants.vcf --exclude-types snps > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpKlDq4E/S1-variants-indel.vcf | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: bgzip S1-variants-snp.vcf | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bgzip -c /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants-snp.vcf > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmprpr0Zu/S1-variants-snp.vcf.gz | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: tabix index S1-variants-snp.vcf.gz | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpOQcTqm/S1-variants-snp.vcf.gz | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: bgzip S1-variants-indel.vcf | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bgzip -c /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants-indel.vcf > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpD2gST2/S1-variants-indel.vcf.gz | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: tabix index S1-variants-indel.vcf.gz | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpt25dtC/S1-variants-indel.vcf.gz | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: Combine variant files | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen-commands: /usr/local/bin/gatk-framework -Xms500m -Xmx3500m -XX:+UseSerialGC -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --out /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpxw2zh2/S1-variants-merge.vcf.gz --variant:v0 /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants-snp.vcf.gz --variant:v1 /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants-indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:28,094 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:28,096 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53 | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:28,097 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:28,097 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:28,100 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --out /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpxw2zh2/S1-variants-merge.vcf.gz --variant:v0 /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants-snp.vcf.gz --variant:v1 /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants-indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:28,102 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:28,103 HelpFormatter - Date/Time: 2014/10/03 19:08:28 | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:28,103 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:28,104 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:28,593 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:28,645 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: WARN 19:08:28,685 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: WARN 19:08:28,686 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:28,742 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:28,743 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:28,744 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:28,745 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:28,746 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:28,823 ProgressMeter - done 12.0 0.0 s 106.5 m 45.7% 0.0 s 0.0 s | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: INFO 19:08:28,824 ProgressMeter - Total runtime 0.08 secs, 0.00 min, 0.00 hours | |
| ok | |
| Select a sample from a VCF file. ... [2014-10-03 19:08] DEBUG: bcbio-nextgen: Select sample: S2 | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bcftools view -O z /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined.vcf.gz -s S2 > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpsVLXID/S1_S2-combined-sampleselect.vcf.gz | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen: tabix index S1_S2-combined-sampleselect.vcf.gz | |
| [2014-10-03 19:08] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpxYJXIJ/S1_S2-combined-sampleselect.vcf.gz | |
| ok | |
| Ensure we can correctly find paired fastq files. ... ok | |
| ---------------------------------------------------------------------- | |
| Ran 11 tests in 292.784s | |
| OK | |
| vagrant@vagrant-ubuntu-trusty-64:~/bcbio-nextgen/tests$ exit | |
| logout | |
| Connection to 127.0.0.1 closed. | |
| christophes-pro:bcbio pfaucon$ vagrant halt | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| ==> default: Attempting graceful shutdown of VM... | |
| nano Vagra | |
| christophes-pro:bcbio pfaucon$ nano Vagrantfile | |
| christophes-pro:bcbio pfaucon$ vagrant up | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| Bringing machine 'default' up with 'virtualbox' provider... | |
| ==> default: Checking if box 'ubuntu/trusty64' is up to date... | |
| ==> default: Clearing any previously set forwarded ports... | |
| ==> default: Clearing any previously set network interfaces... | |
| ==> default: Preparing network interfaces based on configuration... | |
| default: Adapter 1: nat | |
| ==> default: Forwarding ports... | |
| default: 8090 => 8090 (adapter 1) | |
| default: 22 => 2222 (adapter 1) | |
| ==> default: Running 'pre-boot' VM customizations... | |
| ==> default: Booting VM... | |
| ==> default: Waiting for machine to boot. This may take a few minutes... | |
| default: SSH address: 127.0.0.1:2222 | |
| default: SSH username: vagrant | |
| default: SSH auth method: private key | |
| default: Warning: Connection timeout. Retrying... | |
| ==> default: Machine booted and ready! | |
| ==> default: Checking for guest additions in VM... | |
| ==> default: Mounting shared folders... | |
| default: /vagrant => /Volumes/WORK/vagrant/bcbio | |
| default: /vagrant_data => /Volumes/WORK/rnaseq | |
| ==> default: Machine already provisioned. Run `vagrant provision` or use the `--provision` | |
| ==> default: to force provisioning. Provisioners marked to run always will still run. | |
| christophes-pro:bcbio pfaucon$ vagrant ssh | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| Welcome to Ubuntu 14.04.1 LTS (GNU/Linux 3.13.0-35-generic x86_64) | |
| * Documentation: https://help.ubuntu.com/ | |
| System information as of Fri Oct 3 19:24:08 UTC 2014 | |
| System load: 0.15 Processes: 110 | |
| Usage of /: 73.8% of 39.34GB Users logged in: 0 | |
| Memory usage: 1% IP address for eth0: 10.0.2.15 | |
| Swap usage: 0% | |
| Graph this data and manage this system at: | |
| https://landscape.canonical.com/ | |
| Get cloud support with Ubuntu Advantage Cloud Guest: | |
| http://www.ubuntu.com/business/services/cloud | |
| Last login: Fri Oct 3 19:03:25 2014 from 10.0.2.2 | |
| vagrant@vagrant-ubuntu-trusty-64:~$ top | |
| top - 19:24:40 up 0 min, 1 user, load average: 0.23, 0.06, 0.02 | |
| Tasks: 102 total, 2 running, 100 sleeping, 0 stopped, 0 zombie | |
| %Cpu(s): 0.0 us, 0.0 sy, 0.0 ni,100.0 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st | |
| KiB Mem: 16434280 total, 443004 used, 15991276 free, 16444 buffers | |
| KiB Swap: 0 total, 0 used, 0 free. 212112 cached Mem | |
| PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND | |
| 1 root 20 0 33640 2932 1496 S 0.0 0.0 0:00.89 init | |
| 2 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kthreadd | |
| 3 root 20 0 0 0 0 S 0.0 0.0 0:00.10 ksoftirqd/0 | |
| 4 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kworker/0:0 | |
| 5 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kworker/0:0H | |
| 6 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kworker/u8:0 | |
| 7 root 20 0 0 0 0 S 0.0 0.0 0:00.15 rcu_sched | |
| 8 root 20 0 0 0 0 R 0.0 0.0 0:00.15 rcuos/0 | |
| 9 root 20 0 0 0 0 S 0.0 0.0 0:00.08 rcuos/1 | |
| 10 root 20 0 0 0 0 S 0.0 0.0 0:00.09 rcuos/2 | |
| 11 root 20 0 0 0 0 S 0.0 0.0 0:00.10 rcuos/3 | |
| 12 root 20 0 0 0 0 S 0.0 0.0 0:00.00 rcu_bh | |
| 13 root 20 0 0 0 0 S 0.0 0.0 0:00.00 rcuob/0 | |
| 14 root 20 0 0 0 0 S 0.0 0.0 0:00.00 rcuob/1 | |
| 15 root 20 0 0 0 0 S 0.0 0.0 0:00.00 rcuob/2 | |
| 16 root 20 0 0 0 0 S 0.0 0.0 0:00.00 rcuob/3 | |
| 17 root rt 0 0 0 0 S 0.0 0.0 0:00.01 migration/0 | |
| 18 root rt 0 0 0 0 S 0.0 0.0 0:00.00 watchdog/0 | |
| 19 root rt 0 0 0 0 S 0.0 0.0 0:00.00 watchdog/1 | |
| 20 root rt 0 0 0 0 S 0.0 0.0 0:00.01 migration/1 | |
| 21 root 20 0 0 0 0 S 0.0 0.0 0:00.00 ksoftirqd/1 | |
| 22 root 20 0 0 0 0 S 0.0 0.0 0:00.01 kworker/1:0 | |
| 23 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kworker/1:0H | |
| 24 root rt 0 0 0 0 S 0.0 0.0 0:00.00 watchdog/2 | |
| 25 root rt 0 0 0 0 S 0.0 0.0 0:00.06 migration/2 | |
| 26 root 20 0 0 0 0 S 0.0 0.0 0:00.00 ksoftirqd/2 | |
| 27 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kworker/2:0 | |
| 28 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kworker/2:0H | |
| 29 root rt 0 0 0 0 S 0.0 0.0 0:00.00 watchdog/3 | |
| 30 root rt 0 0 0 0 S 0.0 0.0 0:00.01 migration/3 | |
| 31 root 20 0 0 0 0 S 0.0 0.0 0:00.00 ksoftirqd/3 | |
| 32 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kworker/3:0 | |
| 33 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kworker/3:0H | |
| 34 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 khelper | |
| 35 root 20 0 0 0 0 S 0.0 0.0 0:00.01 kdevtmpfs | |
| 36 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 netns | |
| 37 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 writeback | |
| vagrant@vagrant-ubuntu-trusty-64:~$ | |
| vagrant@vagrant-ubuntu-trusty-64:~$ | |
| vagrant@vagrant-ubuntu-trusty-64:~$ nproc | |
| 4 | |
| vagrant@vagrant-ubuntu-trusty-64:~$ exit | |
| logout | |
| Connection to 127.0.0.1 closed. | |
| christophes-pro:bcbio pfaucon$ vagrant halt | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| ==> default: Attempting graceful shutdown of VM... | |
| ^[[A^[[A^[[A^[[B^[[Bchristophes-pro:bcbio pfaucon$ nano Vagrantfile | |
| christophes-pro:bcbio pfaucon$ vagrant up && vagrant ssh | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| Bringing machine 'default' up with 'virtualbox' provider... | |
| ==> default: Checking if box 'ubuntu/trusty64' is up to date... | |
| ==> default: Clearing any previously set forwarded ports... | |
| ==> default: Clearing any previously set network interfaces... | |
| ==> default: Preparing network interfaces based on configuration... | |
| default: Adapter 1: nat | |
| ==> default: Forwarding ports... | |
| default: 8090 => 8090 (adapter 1) | |
| default: 22 => 2222 (adapter 1) | |
| ==> default: Running 'pre-boot' VM customizations... | |
| ==> default: Booting VM... | |
| ==> default: Waiting for machine to boot. This may take a few minutes... | |
| default: SSH address: 127.0.0.1:2222 | |
| default: SSH username: vagrant | |
| default: SSH auth method: private key | |
| default: Warning: Connection timeout. Retrying... | |
| ==> default: Machine booted and ready! | |
| ==> default: Checking for guest additions in VM... | |
| ==> default: Mounting shared folders... | |
| default: /vagrant => /Volumes/WORK/vagrant/bcbio | |
| default: /vagrant_data => /Volumes/WORK/rnaseq | |
| ==> default: Machine already provisioned. Run `vagrant provision` or use the `--provision` | |
| ==> default: to force provisioning. Provisioners marked to run always will still run. | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| Welcome to Ubuntu 14.04.1 LTS (GNU/Linux 3.13.0-35-generic x86_64) | |
| * Documentation: https://help.ubuntu.com/ | |
| System information as of Fri Oct 3 19:26:11 UTC 2014 | |
| System load: 0.88 Processes: 142 | |
| Usage of /: 73.8% of 39.34GB Users logged in: 0 | |
| Memory usage: 1% IP address for eth0: 10.0.2.15 | |
| Swap usage: 0% | |
| Graph this data and manage this system at: | |
| https://landscape.canonical.com/ | |
| Get cloud support with Ubuntu Advantage Cloud Guest: | |
| http://www.ubuntu.com/business/services/cloud | |
| Last login: Fri Oct 3 19:24:19 2014 from 10.0.2.2 | |
| vagrant@vagrant-ubuntu-trusty-64:~$ ls | |
| bcbio-nextgen gatk gatk2 Library tmp | |
| vagrant@vagrant-ubuntu-trusty-64:~$ cd /vagrant_data/ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ wget https://raw.github.com/chapmanb/bcbio-nextgen/master/config/examples/rnaseq-seqc-getdata.sh | |
| --2014-10-03 19:27:22-- https://raw.github.com/chapmanb/bcbio-nextgen/master/config/examples/rnaseq-seqc-getdata.sh | |
| Resolving raw.github.com (raw.github.com)... 199.27.79.133 | |
| Connecting to raw.github.com (raw.github.com)|199.27.79.133|:443... connected. | |
| HTTP request sent, awaiting response... 301 Moved Permanently | |
| Location: https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/examples/rnaseq-seqc-getdata.sh [following] | |
| --2014-10-03 19:27:28-- https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/examples/rnaseq-seqc-getdata.sh | |
| Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 199.27.79.133 | |
| Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|199.27.79.133|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 1024 (1.0K) [text/plain] | |
| Saving to: ‘rnaseq-seqc-getdata.sh’ | |
| 100%[========================================================================================================================>] 1,024 --.-K/s in 0s | |
| 2014-10-03 19:27:28 (40.0 MB/s) - ‘rnaseq-seqc-getdata.sh’ saved [1024/1024] | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ nano rnaseq-seqc-getdata.sh | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ ./rnaseq-seqc-getdata.sh | |
| -bash: ./rnaseq-seqc-getdata.sh: Permission denied | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ sh rnaseq-seqc-getdata.sh | |
| --2014-10-03 19:30:20-- https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/examples/rnaseq-seqc.yaml | |
| Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 23.235.47.133 | |
| Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|23.235.47.133|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 307 [text/plain] | |
| Saving to: ‘rnaseq-seqc.yaml’ | |
| 100%[========================================================================================================================>] 307 --.-K/s in 0s | |
| 2014-10-03 19:30:25 (14.0 MB/s) - ‘rnaseq-seqc.yaml’ saved [307/307] | |
| --2014-10-03 19:30:25-- https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/examples/seqc.csv | |
| Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 23.235.47.133 | |
| Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|23.235.47.133|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 279 [text/plain] | |
| Saving to: ‘seqc.csv’ | |
| 100%[========================================================================================================================>] 279 --.-K/s in 0s | |
| 2014-10-03 19:30:31 (13.4 MB/s) - ‘seqc.csv’ saved [279/279] | |
| description UHRR_rep4 | |
| panel UHRR | |
| description HBRR_rep4 | |
| panel HBRR | |
| description HBRR_rep1 | |
| panel HBRR | |
| description UHRR_rep1 | |
| panel UHRR | |
| description UHRR_rep5 | |
| panel UHRR | |
| description HBRR_rep5 | |
| panel HBRR | |
| description UHRR_rep2 | |
| panel UHRR | |
| description HBRR_rep2 | |
| panel HBRR | |
| description UHRR_rep3 | |
| panel UHRR | |
| description HBRR_rep3 | |
| panel HBRR | |
| Configuration file created at: /vagrant_data/seqc-test/seqc/config/seqc.yaml | |
| Edit to finalize and run with: | |
| cd /vagrant_data/seqc-test/seqc/work | |
| bcbio_nextgen.py ../config/seqc.yaml | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ ls | |
| GenomeAnalysisTK-3.2-2.tar.bz2 Miniconda-3.6.0-MacOSX-x86_64.sh rnaseq-seqc-getdata.sh seqc-test | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ cd seqc-test/ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test$ ls | |
| input rnaseq-seqc.yaml seqc | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test$ ct seqc/ | |
| ct: command not found | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test$ cd seqc/ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc$ ls | |
| config work | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc$ cd ../input/ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ ls | |
| seqc.csv SRR950078_2.log SRR950079_2.log SRR950080_2.log SRR950081_2.log SRR950082_2.log SRR950083_2.log | |
| SRR950078_1.fastq.gz SRR950079_1.fastq.gz SRR950080_1.fastq.gz SRR950081_1.fastq.gz SRR950082_1.fastq.gz SRR950083_1.fastq.gz | |
| SRR950078_1.log SRR950079_1.log SRR950080_1.log SRR950081_1.log SRR950082_1.log SRR950083_1.log | |
| SRR950078_2.fastq.gz SRR950079_2.fastq.gz SRR950080_2.fastq.gz SRR950081_2.fastq.gz SRR950082_2.fastq.gz SRR950083_2.fastq.gz | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ cat SRR950078_1.log | |
| --2014-10-03 19:30:25-- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_1.fastq.gz | |
| => ‘SRR950078_1.fastq.gz’ | |
| Resolving ftp.sra.ebi.ac.uk (ftp.sra.ebi.ac.uk)... 193.62.197.89 | |
| Connecting to ftp.sra.ebi.ac.uk (ftp.sra.ebi.ac.uk)|193.62.197.89|:21... connected. | |
| Logging in as anonymous ... | |
| Error in server response, closing control connection. | |
| Retrying. | |
| --2014-10-03 19:30:32-- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_1.fastq.gz | |
| (try: 2) => ‘SRR950078_1.fastq.gz’ | |
| Connecting to ftp.sra.ebi.ac.uk (ftp.sra.ebi.ac.uk)|193.62.197.89|:21... connected. | |
| Logging in as anonymous ... | |
| Error in server response, closing control connection. | |
| Retrying. | |
| --2014-10-03 19:30:34-- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_1.fastq.gz | |
| (try: 3) => ‘SRR950078_1.fastq.gz’ | |
| Connecting to ftp.sra.ebi.ac.uk (ftp.sra.ebi.ac.uk)|193.62.197.89|:21... connected. | |
| Logging in as anonymous ... | |
| Error in server response, closing control connection. | |
| Retrying. | |
| --2014-10-03 19:30:38-- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_1.fastq.gz | |
| (try: 4) => ‘SRR950078_1.fastq.gz’ | |
| Connecting to ftp.sra.ebi.ac.uk (ftp.sra.ebi.ac.uk)|193.62.197.89|:21... connected. | |
| Logging in as anonymous ... | |
| Error in server response, closing control connection. | |
| Retrying. | |
| --2014-10-03 19:30:42-- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_1.fastq.gz | |
| (try: 5) => ‘SRR950078_1.fastq.gz’ | |
| Connecting to ftp.sra.ebi.ac.uk (ftp.sra.ebi.ac.uk)|193.62.197.89|:21... connected. | |
| Logging in as anonymous ... | |
| Error in server response, closing control connection. | |
| Retrying. | |
| --2014-10-03 19:30:48-- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_1.fastq.gz | |
| (try: 6) => ‘SRR950078_1.fastq.gz’ | |
| Connecting to ftp.sra.ebi.ac.uk (ftp.sra.ebi.ac.uk)|193.62.197.89|:21... connected. | |
| Logging in as anonymous ... | |
| Error in server response, closing control connection. | |
| Retrying. | |
| --2014-10-03 19:30:54-- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_1.fastq.gz | |
| (try: 7) => ‘SRR950078_1.fastq.gz’ | |
| Connecting to ftp.sra.ebi.ac.uk (ftp.sra.ebi.ac.uk)|193.62.197.89|:21... connected. | |
| Logging in as anonymous ... | |
| Error in server response, closing control connection. | |
| Retrying. | |
| --2014-10-03 19:31:02-- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_1.fastq.gz | |
| (try: 8) => ‘SRR950078_1.fastq.gz’ | |
| Connecting to ftp.sra.ebi.ac.uk (ftp.sra.ebi.ac.uk)|193.62.197.89|:21... connected. | |
| Logging in as anonymous ... | |
| Error in server response, closing control connection. | |
| Retrying. | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ cat SRR950078_1.log | |
| --2014-10-03 19:30:25-- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_1.fastq.gz | |
| => ‘SRR950078_1.fastq.gz’ | |
| Resolving ftp.sra.ebi.ac.uk (ftp.sra.ebi.ac.uk)... 193.62.197.89 | |
| Connecting to ftp.sra.ebi.ac.uk (ftp.sra.ebi.ac.uk)|193.62.197.89|:21... connected. | |
| Logging in as anonymous ... | |
| Error in server response, closing control connection. | |
| Retrying. | |
| --2014-10-03 19:30:32-- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_1.fastq.gz | |
| (try: 2) => ‘SRR950078_1.fastq.gz’ | |
| Connecting to ftp.sra.ebi.ac.uk (ftp.sra.ebi.ac.uk)|193.62.197.89|:21... connected. | |
| Logging in as anonymous ... | |
| Error in server response, closing control connection. | |
| Retrying. | |
| --2014-10-03 19:30:34-- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_1.fastq.gz | |
| (try: 3) => ‘SRR950078_1.fastq.gz’ | |
| Connecting to ftp.sra.ebi.ac.uk (ftp.sra.ebi.ac.uk)|193.62.197.89|:21... connected. | |
| Logging in as anonymous ... | |
| Error in server response, closing control connection. | |
| Retrying. | |
| --2014-10-03 19:30:38-- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_1.fastq.gz | |
| (try: 4) => ‘SRR950078_1.fastq.gz’ | |
| Connecting to ftp.sra.ebi.ac.uk (ftp.sra.ebi.ac.uk)|193.62.197.89|:21... connected. | |
| Logging in as anonymous ... | |
| Error in server response, closing control connection. | |
| Retrying. | |
| --2014-10-03 19:30:42-- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_1.fastq.gz | |
| (try: 5) => ‘SRR950078_1.fastq.gz’ | |
| Connecting to ftp.sra.ebi.ac.uk (ftp.sra.ebi.ac.uk)|193.62.197.89|:21... connected. | |
| Logging in as anonymous ... | |
| Error in server response, closing control connection. | |
| Retrying. | |
| --2014-10-03 19:30:48-- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_1.fastq.gz | |
| (try: 6) => ‘SRR950078_1.fastq.gz’ | |
| Connecting to ftp.sra.ebi.ac.uk (ftp.sra.ebi.ac.uk)|193.62.197.89|:21... connected. | |
| Logging in as anonymous ... | |
| Error in server response, closing control connection. | |
| Retrying. | |
| --2014-10-03 19:30:54-- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_1.fastq.gz | |
| (try: 7) => ‘SRR950078_1.fastq.gz’ | |
| Connecting to ftp.sra.ebi.ac.uk (ftp.sra.ebi.ac.uk)|193.62.197.89|:21... connected. | |
| Logging in as anonymous ... | |
| Error in server response, closing control connection. | |
| Retrying. | |
| --2014-10-03 19:31:02-- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_1.fastq.gz | |
| (try: 8) => ‘SRR950078_1.fastq.gz’ | |
| Connecting to ftp.sra.ebi.ac.uk (ftp.sra.ebi.ac.uk)|193.62.197.89|:21... connected. | |
| Logging in as anonymous ... | |
| Error in server response, closing control connection. | |
| Retrying. | |
| --2014-10-03 19:31:10-- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_1.fastq.gz | |
| (try: 9) => ‘SRR950078_1.fastq.gz’ | |
| Connecting to ftp.sra.ebi.ac.uk (ftp.sra.ebi.ac.uk)|193.62.197.89|:21... connected. | |
| Logging in as anonymous ... | |
| Error in server response, closing control connection. | |
| Retrying. | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ ls -al | |
| total 134720 | |
| drwxr-xr-x 1 vagrant vagrant 918 Oct 3 19:30 . | |
| drwxr-xr-x 1 vagrant vagrant 170 Oct 3 19:30 .. | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:30 seqc.csv | |
| -rw-r--r-- 1 vagrant vagrant 0 Oct 3 19:30 SRR950078_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 2918 Oct 3 19:31 SRR950078_1.log | |
| -rw-r--r-- 1 vagrant vagrant 0 Oct 3 19:30 SRR950078_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 2918 Oct 3 19:31 SRR950078_2.log | |
| -rw-r--r-- 1 vagrant vagrant 0 Oct 3 19:30 SRR950079_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 2918 Oct 3 19:31 SRR950079_1.log | |
| -rw-r--r-- 1 vagrant vagrant 0 Oct 3 19:30 SRR950079_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 2918 Oct 3 19:31 SRR950079_2.log | |
| -rw-r--r-- 1 vagrant vagrant 0 Oct 3 19:30 SRR950080_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 2918 Oct 3 19:31 SRR950080_1.log | |
| -rw-r--r-- 1 vagrant vagrant 0 Oct 3 19:30 SRR950080_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 2918 Oct 3 19:31 SRR950080_2.log | |
| -rw-r--r-- 1 vagrant vagrant 72262912 Oct 3 19:31 SRR950081_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 111888 Oct 3 19:31 SRR950081_1.log | |
| -rw-r--r-- 1 vagrant vagrant 0 Oct 3 19:30 SRR950081_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 2918 Oct 3 19:31 SRR950081_2.log | |
| -rw-r--r-- 1 vagrant vagrant 65422688 Oct 3 19:31 SRR950082_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 102219 Oct 3 19:31 SRR950082_1.log | |
| -rw-r--r-- 1 vagrant vagrant 0 Oct 3 19:30 SRR950082_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 2918 Oct 3 19:31 SRR950082_2.log | |
| -rw-r--r-- 1 vagrant vagrant 0 Oct 3 19:30 SRR950083_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 2918 Oct 3 19:31 SRR950083_1.log | |
| -rw-r--r-- 1 vagrant vagrant 0 Oct 3 19:30 SRR950083_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 2918 Oct 3 19:31 SRR950083_2.log | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ ls -al | |
| total 259452 | |
| drwxr-xr-x 1 vagrant vagrant 918 Oct 3 19:30 . | |
| drwxr-xr-x 1 vagrant vagrant 170 Oct 3 19:30 .. | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:30 seqc.csv | |
| -rw-r--r-- 1 vagrant vagrant 0 Oct 3 19:30 SRR950078_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 4186 Oct 3 19:31 SRR950078_1.log | |
| -rw-r--r-- 1 vagrant vagrant 0 Oct 3 19:30 SRR950078_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 4186 Oct 3 19:31 SRR950078_2.log | |
| -rw-r--r-- 1 vagrant vagrant 0 Oct 3 19:30 SRR950079_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 4186 Oct 3 19:31 SRR950079_1.log | |
| -rw-r--r-- 1 vagrant vagrant 0 Oct 3 19:30 SRR950079_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 4186 Oct 3 19:31 SRR950079_2.log | |
| -rw-r--r-- 1 vagrant vagrant 0 Oct 3 19:30 SRR950080_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 4186 Oct 3 19:31 SRR950080_1.log | |
| -rw-r--r-- 1 vagrant vagrant 0 Oct 3 19:30 SRR950080_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 4186 Oct 3 19:31 SRR950080_2.log | |
| -rw-r--r-- 1 vagrant vagrant 125389160 Oct 3 19:31 SRR950081_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 194392 Oct 3 19:31 SRR950081_1.log | |
| -rw-r--r-- 1 vagrant vagrant 0 Oct 3 19:30 SRR950081_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 4186 Oct 3 19:31 SRR950081_2.log | |
| -rw-r--r-- 1 vagrant vagrant 139783736 Oct 3 19:31 SRR950082_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 218176 Oct 3 19:31 SRR950082_1.log | |
| -rw-r--r-- 1 vagrant vagrant 0 Oct 3 19:30 SRR950082_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 4186 Oct 3 19:31 SRR950082_2.log | |
| -rw-r--r-- 1 vagrant vagrant 0 Oct 3 19:30 SRR950083_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 4186 Oct 3 19:31 SRR950083_1.log | |
| -rw-r--r-- 1 vagrant vagrant 0 Oct 3 19:30 SRR950083_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 4186 Oct 3 19:31 SRR950083_2.log | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ cd ../.. | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ ls | |
| GenomeAnalysisTK-3.2-2.tar.bz2 Miniconda-3.6.0-MacOSX-x86_64.sh rnaseq-seqc-getdata.sh seqc-test | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ nano rnaseq-seqc-getdata.sh | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ ps -auxx | |
| USER PID %CPU %MEM VSZ RSS TTY STAT START TIME COMMAND | |
| root 1 0.3 0.0 33628 2964 ? Ss 19:26 0:01 /sbin/init | |
| root 2 0.0 0.0 0 0 ? S 19:26 0:00 [kthreadd] | |
| root 3 0.0 0.0 0 0 ? S 19:26 0:00 [ksoftirqd/0] | |
| root 4 0.0 0.0 0 0 ? S 19:26 0:00 [kworker/0:0] | |
| root 5 0.0 0.0 0 0 ? S< 19:26 0:00 [kworker/0:0H] | |
| root 7 0.1 0.0 0 0 ? S 19:26 0:00 [rcu_sched] | |
| root 8 0.0 0.0 0 0 ? S 19:26 0:00 [rcuos/0] | |
| root 9 0.0 0.0 0 0 ? S 19:26 0:00 [rcuos/1] | |
| root 10 0.0 0.0 0 0 ? S 19:26 0:00 [rcuos/2] | |
| root 11 0.0 0.0 0 0 ? S 19:26 0:00 [rcuos/3] | |
| root 12 0.0 0.0 0 0 ? S 19:26 0:00 [rcuos/4] | |
| root 13 0.0 0.0 0 0 ? S 19:26 0:00 [rcuos/5] | |
| root 14 0.0 0.0 0 0 ? S 19:26 0:00 [rcuos/6] | |
| root 15 0.0 0.0 0 0 ? S 19:26 0:00 [rcuos/7] | |
| root 16 0.0 0.0 0 0 ? S 19:26 0:00 [rcu_bh] | |
| root 17 0.0 0.0 0 0 ? S 19:26 0:00 [rcuob/0] | |
| root 18 0.0 0.0 0 0 ? S 19:26 0:00 [rcuob/1] | |
| root 19 0.0 0.0 0 0 ? S 19:26 0:00 [rcuob/2] | |
| root 20 0.0 0.0 0 0 ? S 19:26 0:00 [rcuob/3] | |
| root 21 0.0 0.0 0 0 ? S 19:26 0:00 [rcuob/4] | |
| root 22 0.0 0.0 0 0 ? S 19:26 0:00 [rcuob/5] | |
| root 23 0.0 0.0 0 0 ? S 19:26 0:00 [rcuob/6] | |
| root 24 0.0 0.0 0 0 ? S 19:26 0:00 [rcuob/7] | |
| root 25 0.0 0.0 0 0 ? S 19:26 0:00 [migration/0] | |
| root 26 0.0 0.0 0 0 ? S 19:26 0:00 [watchdog/0] | |
| root 27 0.0 0.0 0 0 ? S 19:26 0:00 [watchdog/1] | |
| root 28 0.0 0.0 0 0 ? S 19:26 0:00 [migration/1] | |
| root 29 0.0 0.0 0 0 ? S 19:26 0:00 [ksoftirqd/1] | |
| root 30 0.0 0.0 0 0 ? S 19:26 0:00 [kworker/1:0] | |
| root 31 0.0 0.0 0 0 ? S< 19:26 0:00 [kworker/1:0H] | |
| root 32 0.0 0.0 0 0 ? S 19:26 0:00 [watchdog/2] | |
| root 33 0.0 0.0 0 0 ? S 19:26 0:00 [migration/2] | |
| root 34 0.0 0.0 0 0 ? S 19:26 0:00 [ksoftirqd/2] | |
| root 35 0.0 0.0 0 0 ? S 19:26 0:00 [kworker/2:0] | |
| root 36 0.0 0.0 0 0 ? S< 19:26 0:00 [kworker/2:0H] | |
| root 37 0.0 0.0 0 0 ? S 19:26 0:00 [watchdog/3] | |
| root 38 0.0 0.0 0 0 ? S 19:26 0:00 [migration/3] | |
| root 39 0.0 0.0 0 0 ? S 19:26 0:00 [ksoftirqd/3] | |
| root 40 0.0 0.0 0 0 ? S 19:26 0:00 [kworker/3:0] | |
| root 41 0.0 0.0 0 0 ? S< 19:26 0:00 [kworker/3:0H] | |
| root 42 0.0 0.0 0 0 ? S 19:26 0:00 [watchdog/4] | |
| root 43 0.0 0.0 0 0 ? S 19:26 0:00 [migration/4] | |
| root 44 0.0 0.0 0 0 ? S 19:26 0:00 [ksoftirqd/4] | |
| root 45 0.0 0.0 0 0 ? S 19:26 0:00 [kworker/4:0] | |
| root 46 0.0 0.0 0 0 ? S< 19:26 0:00 [kworker/4:0H] | |
| root 47 0.0 0.0 0 0 ? S 19:26 0:00 [watchdog/5] | |
| root 48 0.0 0.0 0 0 ? S 19:26 0:00 [migration/5] | |
| root 49 0.0 0.0 0 0 ? S 19:26 0:00 [ksoftirqd/5] | |
| root 50 0.0 0.0 0 0 ? S 19:26 0:00 [kworker/5:0] | |
| root 51 0.0 0.0 0 0 ? S< 19:26 0:00 [kworker/5:0H] | |
| root 52 0.0 0.0 0 0 ? S 19:26 0:00 [watchdog/6] | |
| root 53 0.0 0.0 0 0 ? S 19:26 0:00 [migration/6] | |
| root 54 0.0 0.0 0 0 ? S 19:26 0:00 [ksoftirqd/6] | |
| root 55 0.0 0.0 0 0 ? S 19:26 0:00 [kworker/6:0] | |
| root 56 0.0 0.0 0 0 ? S< 19:26 0:00 [kworker/6:0H] | |
| root 57 0.0 0.0 0 0 ? S 19:26 0:00 [watchdog/7] | |
| root 58 0.0 0.0 0 0 ? S 19:26 0:00 [migration/7] | |
| root 59 0.0 0.0 0 0 ? S 19:26 0:00 [ksoftirqd/7] | |
| root 60 0.0 0.0 0 0 ? S 19:26 0:00 [kworker/7:0] | |
| root 61 0.0 0.0 0 0 ? S< 19:26 0:00 [kworker/7:0H] | |
| root 62 0.0 0.0 0 0 ? S< 19:26 0:00 [khelper] | |
| root 63 0.0 0.0 0 0 ? S 19:26 0:00 [kdevtmpfs] | |
| root 64 0.0 0.0 0 0 ? S< 19:26 0:00 [netns] | |
| root 65 0.0 0.0 0 0 ? S< 19:26 0:00 [writeback] | |
| root 66 0.0 0.0 0 0 ? S< 19:26 0:00 [kintegrityd] | |
| root 67 0.0 0.0 0 0 ? S< 19:26 0:00 [bioset] | |
| root 68 0.0 0.0 0 0 ? S< 19:26 0:00 [kworker/u17:0] | |
| root 69 0.0 0.0 0 0 ? S< 19:26 0:00 [kblockd] | |
| root 70 0.0 0.0 0 0 ? S< 19:26 0:00 [ata_sff] | |
| root 71 0.0 0.0 0 0 ? S 19:26 0:00 [khubd] | |
| root 72 0.0 0.0 0 0 ? S< 19:26 0:00 [md] | |
| root 73 0.0 0.0 0 0 ? S< 19:26 0:00 [devfreq_wq] | |
| root 74 0.0 0.0 0 0 ? S 19:26 0:00 [kworker/2:1] | |
| root 75 0.0 0.0 0 0 ? S 19:26 0:00 [khungtaskd] | |
| root 76 0.0 0.0 0 0 ? S 19:26 0:00 [kswapd0] | |
| root 77 0.0 0.0 0 0 ? SN 19:26 0:00 [ksmd] | |
| root 78 0.0 0.0 0 0 ? SN 19:26 0:00 [khugepaged] | |
| root 79 0.0 0.0 0 0 ? S 19:26 0:00 [fsnotify_mark] | |
| root 80 0.0 0.0 0 0 ? S 19:26 0:00 [ecryptfs-kthrea] | |
| root 81 0.0 0.0 0 0 ? S< 19:26 0:00 [crypto] | |
| root 93 0.0 0.0 0 0 ? S< 19:26 0:00 [kthrotld] | |
| root 94 0.0 0.0 0 0 ? S 19:26 0:00 [kworker/1:1] | |
| root 95 0.0 0.0 0 0 ? S 19:26 0:00 [kworker/u16:1] | |
| root 96 0.0 0.0 0 0 ? S 19:26 0:00 [kworker/0:1] | |
| root 115 0.0 0.0 0 0 ? S< 19:26 0:00 [deferwq] | |
| root 116 0.0 0.0 0 0 ? S< 19:26 0:00 [charger_manager] | |
| root 118 0.0 0.0 0 0 ? S 19:26 0:00 [kworker/4:1] | |
| root 141 0.0 0.0 0 0 ? S 19:26 0:00 [kworker/3:1] | |
| root 160 0.0 0.0 0 0 ? S 19:26 0:00 [scsi_eh_0] | |
| root 163 0.0 0.0 0 0 ? S 19:26 0:00 [kworker/u16:2] | |
| root 164 0.0 0.0 0 0 ? S< 19:26 0:00 [kpsmoused] | |
| root 165 0.0 0.0 0 0 ? S 19:26 0:00 [kworker/6:1] | |
| root 176 0.0 0.0 0 0 ? S 19:26 0:00 [kworker/5:1] | |
| root 211 0.0 0.0 0 0 ? S 19:26 0:00 [jbd2/sda1-8] | |
| root 212 0.0 0.0 0 0 ? S< 19:26 0:00 [ext4-rsv-conver] | |
| root 225 0.0 0.0 0 0 ? S 19:26 0:00 [kworker/7:1] | |
| root 453 0.0 0.0 19740 916 ? S 19:26 0:00 upstart-udev-bridge --daemon | |
| root 457 0.0 0.0 49852 1628 ? Ss 19:26 0:00 /lib/systemd/systemd-udevd --daemon | |
| root 496 0.0 0.0 0 0 ? S< 19:26 0:00 [iprt] | |
| root 615 0.0 0.0 23420 1108 ? Ss 19:26 0:00 rpcbind | |
| root 625 0.0 0.0 10224 2412 ? Ss 19:26 0:00 dhclient -1 -v -pf /run/dhclient.eth0.pid -lf /var/lib/dhcp/dhclient.eth0.leases eth0 | |
| statd 656 0.0 0.0 21544 1380 ? Ss 19:26 0:00 rpc.statd -L | |
| root 711 0.0 0.0 15392 680 ? S 19:26 0:00 upstart-socket-bridge --daemon | |
| root 792 0.0 0.0 0 0 ? S< 19:26 0:00 [rpciod] | |
| root 817 0.0 0.0 0 0 ? S< 19:26 0:00 [nfsiod] | |
| message+ 842 0.0 0.0 39184 1240 ? Ss 19:26 0:00 dbus-daemon --system --fork | |
| root 846 0.0 0.0 25544 428 ? Ss 19:26 0:00 rpc.idmapd | |
| root 888 0.0 0.0 43452 1784 ? Ss 19:26 0:00 /lib/systemd/systemd-logind | |
| syslog 908 0.0 0.0 257912 1392 ? Ssl 19:26 0:00 rsyslogd | |
| root 965 0.0 0.0 15276 636 ? S 19:26 0:00 upstart-file-bridge --daemon | |
| root 983 0.0 0.0 14540 956 tty4 Ss+ 19:26 0:00 /sbin/getty -8 38400 tty4 | |
| root 986 0.0 0.0 14540 956 tty5 Ss+ 19:26 0:00 /sbin/getty -8 38400 tty5 | |
| root 991 0.0 0.0 14540 956 tty2 Ss+ 19:26 0:00 /sbin/getty -8 38400 tty2 | |
| root 992 0.0 0.0 14540 948 tty3 Ss+ 19:26 0:00 /sbin/getty -8 38400 tty3 | |
| root 994 0.0 0.0 14540 960 tty6 Ss+ 19:26 0:00 /sbin/getty -8 38400 tty6 | |
| root 1016 0.0 0.0 23656 900 ? Ss 19:26 0:00 cron | |
| daemon 1017 0.0 0.0 19140 160 ? Ss 19:26 0:00 atd | |
| root 1022 0.0 0.0 61364 3060 ? Ss 19:26 0:00 /usr/sbin/sshd -D | |
| root 1069 0.0 0.0 216612 1064 ? Sl 19:26 0:00 /usr/sbin/VBoxService | |
| root 1081 0.0 0.0 4368 660 ? Ss 19:26 0:00 acpid -c /etc/acpi/events -s /var/run/acpid.socket | |
| root 1096 0.0 0.2 182528 34424 ? Ssl 19:26 0:00 /usr/bin/ruby /usr/bin/puppet agent | |
| root 1133 0.0 0.2 112780 34524 ? Sl 19:26 0:00 ruby /usr/bin/chef-client -d -P /var/run/chef/client.pid -c /etc/chef/client.rb -i 1800 -s 20 -L | |
| root 1144 0.0 0.0 0 0 ? S< 19:26 0:00 [kworker/u17:1] | |
| root 1161 0.0 0.0 14540 944 tty1 Ss+ 19:26 0:00 /sbin/getty -8 38400 tty1 | |
| root 1191 0.0 0.0 0 0 ? S 19:26 0:00 [kauditd] | |
| root 2280 0.0 0.0 107696 4256 ? Ss 19:26 0:00 sshd: vagrant [priv] | |
| vagrant 2333 0.0 0.0 107696 2192 ? R 19:26 0:00 sshd: vagrant@pts/0 | |
| vagrant 2334 0.0 0.0 23064 5648 pts/0 Ss 19:26 0:00 -bash | |
| vagrant 2529 11.1 0.0 29612 1940 pts/0 S 19:30 0:20 wget -O SRR950081_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950081/SRR950081_1.fast | |
| vagrant 2531 12.2 0.0 29612 1940 pts/0 S 19:30 0:22 wget -O SRR950082_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950082/SRR950082_1.fast | |
| vagrant 2610 0.0 0.0 17168 1296 pts/0 R+ 19:33 0:00 ps -auxx | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ kill -9 2529 | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ kill -9 2531 | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ nano | |
| GenomeAnalysisTK-3.2-2.tar.bz2 Miniconda-3.6.0-MacOSX-x86_64.sh rnaseq-seqc-getdata.sh seqc-test/ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ nano rnaseq-seqc-getdata.sh | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ sh rnaseq-seqc-getdata.sh | |
| --2014-10-03 19:39:17-- https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/examples/rnaseq-seqc.yaml | |
| Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 23.235.47.133 | |
| Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|23.235.47.133|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 307 [text/plain] | |
| Saving to: ‘rnaseq-seqc.yaml.1’ | |
| 100%[========================================================================================================================>] 307 --.-K/s in 0s | |
| 2014-10-03 19:39:22 (14.5 MB/s) - ‘rnaseq-seqc.yaml.1’ saved [307/307] | |
| rnaseq-seqc-getdata.sh: 12: rnaseq-seqc-getdata.sh: Syntax error: "(" unexpected | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ nano rnaseq-seqc-getdata.sh | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ sh rnaseq-seqc-getdata.sh | |
| --2014-10-03 19:41:07-- https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/examples/rnaseq-seqc.yaml | |
| Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 199.27.79.133 | |
| Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|199.27.79.133|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 307 [text/plain] | |
| Saving to: ‘rnaseq-seqc.yaml.2’ | |
| 100%[========================================================================================================================>] 307 --.-K/s in 0s | |
| 2014-10-03 19:41:12 (15.4 MB/s) - ‘rnaseq-seqc.yaml.2’ saved [307/307] | |
| rnaseq-seqc-getdata.sh: 12: rnaseq-seqc-getdata.sh: Syntax error: "(" unexpected | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ nano rnaseq-seqc-getdata.sh | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ ls | |
| GenomeAnalysisTK-3.2-2.tar.bz2 Miniconda-3.6.0-MacOSX-x86_64.sh rnaseq-seqc-getdata.sh seqc-test | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ wget https://raw.github.com/chapmanb/bcbio-nextgen/master/config/examples/rnaseq-seqc-getdata.sh | |
| --2014-10-03 19:42:09-- https://raw.github.com/chapmanb/bcbio-nextgen/master/config/examples/rnaseq-seqc-getdata.sh | |
| Resolving raw.github.com (raw.github.com)... 199.27.79.133 | |
| Connecting to raw.github.com (raw.github.com)|199.27.79.133|:443... connected. | |
| HTTP request sent, awaiting response... 301 Moved Permanently | |
| Location: https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/examples/rnaseq-seqc-getdata.sh [following] | |
| --2014-10-03 19:42:14-- https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/examples/rnaseq-seqc-getdata.sh | |
| Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 199.27.79.133 | |
| Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|199.27.79.133|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 1024 (1.0K) [text/plain] | |
| Saving to: ‘rnaseq-seqc-getdata.sh.1’ | |
| 100%[========================================================================================================================>] 1,024 --.-K/s in 0s | |
| 2014-10-03 19:42:14 (43.0 MB/s) - ‘rnaseq-seqc-getdata.sh.1’ saved [1024/1024] | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ bash rnaseq-seqc-getdata.sh | |
| --2014-10-03 19:42:16-- https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/examples/rnaseq-seqc.yaml | |
| Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 199.27.79.133 | |
| Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|199.27.79.133|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 307 [text/plain] | |
| Saving to: ‘rnaseq-seqc.yaml.3’ | |
| 100%[========================================================================================================================>] 307 --.-K/s in 0s | |
| 2014-10-03 19:42:21 (2.57 MB/s) - ‘rnaseq-seqc.yaml.3’ saved [307/307] | |
| rnaseq-seqc-getdata.sh: line 18: ${$urls}: bad substitution | |
| --2014-10-03 19:42:21-- https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/examples/seqc.csv | |
| Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 199.27.79.133 | |
| Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|199.27.79.133|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 279 [text/plain] | |
| Saving to: ‘seqc.csv.1’ | |
| 100%[========================================================================================================================>] 279 --.-K/s in 0s | |
| 2014-10-03 19:42:26 (14.3 MB/s) - ‘seqc.csv.1’ saved [279/279] | |
| description UHRR_rep4 | |
| panel UHRR | |
| description HBRR_rep4 | |
| panel HBRR | |
| description HBRR_rep1 | |
| panel HBRR | |
| description UHRR_rep1 | |
| panel UHRR | |
| description UHRR_rep5 | |
| panel UHRR | |
| description HBRR_rep5 | |
| panel HBRR | |
| description UHRR_rep2 | |
| panel UHRR | |
| description HBRR_rep2 | |
| panel HBRR | |
| description UHRR_rep3 | |
| panel UHRR | |
| description HBRR_rep3 | |
| panel HBRR | |
| Template configuration file created at: /vagrant_data/seqc-test/seqc/config/seqc-template.yaml | |
| Edit to finalize custom options, then prepare full sample config with: | |
| bcbio_nextgen.py -w template /vagrant_data/seqc-test/seqc/config/seqc-template.yaml seqc sample1.bam sample2.fq | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ nano rnaseq-seqc-getdata.sh | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ nano rnaseq-seqc-getdata.sh | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ nano rnaseq-seqc-getdata.sh | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ wget https://raw.github.com/chapmanb/bcbio-nextgen/master/config/examples/rnaseq-seqc-getdata.sh | |
| --2014-10-03 21:09:06-- https://raw.github.com/chapmanb/bcbio-nextgen/master/config/examples/rnaseq-seqc-getdata.sh | |
| Resolving raw.github.com (raw.github.com)... ^C | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ bash rnaseq-seqc-getdata.sh | |
| rnaseq-seqc-getdata.sh: line 18: ${$urls}: bad substitution | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ nano rnaseq-seqc-getdata.sh | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ bash rnaseq-seqc-getdata.sh | |
| SRR950078_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_1.fastq.gz | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ nano rnaseq-seqc-getdata.sh | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ bash rnaseq-seqc-getdata.sh | |
| {SAMPLE}_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_1.fastq.gz {SAMPLE}_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_2.fastq.gz {SAMPLE}_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950079/SRR950079_1.fastq.gz {SAMPLE}_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950079/SRR950079_2.fastq.gz {SAMPLE}_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950080/SRR950080_1.fastq.gz {SAMPLE}_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950080/SRR950080_2.fastq.gz {SAMPLE}_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950081/SRR950081_1.fastq.gz {SAMPLE}_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950081/SRR950081_2.fastq.gz {SAMPLE}_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950082/SRR950082_1.fastq.gz {SAMPLE}_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950082/SRR950082_2.fastq.gz {SAMPLE}_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950083/SRR950083_1.fastq.gz {SAMPLE}_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950083/SRR950083_2.fastq.gz | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ nano rnaseq-seqc-getdata.sh | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ bash rnaseq-seqc-getdata.sh | |
| SRR950078_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_1.fastq.gz SRR950078_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950078/SRR950078_2.fastq.gz SRR950079_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950079/SRR950079_1.fastq.gz SRR950079_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950079/SRR950079_2.fastq.gz SRR950080_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950080/SRR950080_1.fastq.gz SRR950080_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950080/SRR950080_2.fastq.gz SRR950081_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950081/SRR950081_1.fastq.gz SRR950081_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950081/SRR950081_2.fastq.gz SRR950082_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950082/SRR950082_1.fastq.gz SRR950082_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950082/SRR950082_2.fastq.gz SRR950083_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950083/SRR950083_1.fastq.gz SRR950083_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950083/SRR950083_2.fastq.gz | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ nano rnaseq-seqc-getdata.sh | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ bash rnaseq-seqc-getdata.sh | |
| xargs: wget: terminated by signal 9 | |
| rnaseq-seqc-getdata.sh: line 19: 3264 Done echo "${urls[@]}" | |
| 3265 Killed | xargs -n 1 -P 2 wget -q | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ | |
| Broadcast message from vagrant@vagrant-ubuntu-trusty-64 | |
| (unknown) at 2:52 ... | |
| The system is going down for halt NOW! | |
| Connection to 127.0.0.1 closed by remote host. | |
| Connection to 127.0.0.1 closed. | |
| christophes-pro:bcbio pfaucon$ | |
| [Restored] | |
| Last login: Fri Oct 3 20:17:40 on ttys001 | |
| Christophes-Mac-Pro:bcbio pfaucon$ pwd | |
| /Users/pfaucon/WORK/vagrant/bcbio | |
| Christophes-Mac-Pro:bcbio pfaucon$ vagrant up | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| Bringing machine 'default' up with 'virtualbox' provider... | |
| ==> default: Checking if box 'ubuntu/trusty64' is up to date... | |
| ==> default: Clearing any previously set forwarded ports... | |
| ==> default: Clearing any previously set network interfaces... | |
| ==> default: Preparing network interfaces based on configuration... | |
| default: Adapter 1: nat | |
| ==> default: Forwarding ports... | |
| default: 8090 => 8090 (adapter 1) | |
| default: 22 => 2222 (adapter 1) | |
| ==> default: Running 'pre-boot' VM customizations... | |
| ==> default: Booting VM... | |
| ==> default: Waiting for machine to boot. This may take a few minutes... | |
| default: SSH address: 127.0.0.1:2222 | |
| default: SSH username: vagrant | |
| default: SSH auth method: private key | |
| default: Warning: Connection timeout. Retrying... | |
| default: Warning: Remote connection disconnect. Retrying... | |
| ==> default: Machine booted and ready! | |
| ==> default: Checking for guest additions in VM... | |
| ==> default: Mounting shared folders... | |
| default: /vagrant => /Volumes/WORK/vagrant/bcbio | |
| default: /vagrant_data => /Volumes/WORK/rnaseq | |
| ==> default: Machine already provisioned. Run `vagrant provision` or use the `--provision` | |
| ==> default: to force provisioning. Provisioners marked to run always will still run. | |
| Christophes-Mac-Pro:bcbio pfaucon$ vagrant ssh | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| Welcome to Ubuntu 14.04.1 LTS (GNU/Linux 3.13.0-35-generic x86_64) | |
| * Documentation: https://help.ubuntu.com/ | |
| System information as of Sat Oct 4 03:18:33 UTC 2014 | |
| System load: 0.55 Processes: 170 | |
| Usage of /: 73.8% of 39.34GB Users logged in: 0 | |
| Memory usage: 1% IP address for eth0: 10.0.2.15 | |
| Swap usage: 0% | |
| Graph this data and manage this system at: | |
| https://landscape.canonical.com/ | |
| Get cloud support with Ubuntu Advantage Cloud Guest: | |
| http://www.ubuntu.com/business/services/cloud | |
| Last login: Fri Oct 3 19:34:15 2014 from 10.0.2.2 | |
| vagrant@vagrant-ubuntu-trusty-64:~$ cd /vagrant_data/seqc-test/ | |
| input/ seqc/ | |
| vagrant@vagrant-ubuntu-trusty-64:~$ cd /vagrant_data/seqc-test/input/ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ ls | |
| index.html seqc.csv.1 SRR950079_1.fastq.gz SRR950080_2.fastq.gz SRR950082_1.fastq.gz | |
| index.html.1 SRR950078_1.fastq.gz SRR950079_2.fastq.gz SRR950081_1.fastq.gz SRR950082_2.fastq.gz | |
| seqc.csv SRR950078_2.fastq.gz SRR950080_1.fastq.gz SRR950081_2.fastq.gz | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ ls -al | |
| total 69811376 | |
| drwxr-xr-x 1 vagrant vagrant 544 Oct 4 03:21 . | |
| drwxr-xr-x 1 vagrant vagrant 272 Oct 3 19:42 .. | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html.1 | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:30 seqc.csv | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:42 seqc.csv.1 | |
| -rw-r--r-- 1 vagrant vagrant 8584375694 Oct 3 22:43 SRR950078_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 8650136401 Oct 3 22:28 SRR950078_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9414809474 Oct 3 23:58 SRR950079_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9508216711 Oct 4 00:10 SRR950079_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7845415151 Oct 4 01:08 SRR950080_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7912973223 Oct 4 01:12 SRR950080_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9661234164 Oct 4 02:41 SRR950081_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9758348136 Oct 4 02:36 SRR950081_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 58869888 Oct 4 03:26 SRR950082_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 92434528 Oct 4 03:26 SRR950082_2.fastq.gz | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ ls -al | |
| total 92941972 | |
| drwxr-xr-x 1 vagrant vagrant 680 Oct 4 08:57 . | |
| drwxr-xr-x 1 vagrant vagrant 272 Oct 3 19:42 .. | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html.1 | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 08:17 index.html.2 | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 08:57 index.html.3 | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:30 seqc.csv | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:42 seqc.csv.1 | |
| -rw-r--r-- 1 vagrant vagrant 8584375694 Oct 3 22:43 SRR950078_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 8650136401 Oct 3 22:28 SRR950078_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9414809474 Oct 3 23:58 SRR950079_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9508216711 Oct 4 00:10 SRR950079_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7845415151 Oct 4 01:08 SRR950080_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7912973223 Oct 4 01:12 SRR950080_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9661234164 Oct 4 02:41 SRR950081_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9758348136 Oct 4 02:36 SRR950081_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5632947596 Oct 4 08:57 SRR950082_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5695733721 Oct 4 08:17 SRR950082_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9673029260 Oct 4 13:46 SRR950083_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 2835313400 Oct 4 15:31 SRR950083_2.fastq.gz | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ ls -al | |
| total 92999292 | |
| drwxr-xr-x 1 vagrant vagrant 680 Oct 4 08:57 . | |
| drwxr-xr-x 1 vagrant vagrant 272 Oct 3 19:42 .. | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html.1 | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 08:17 index.html.2 | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 08:57 index.html.3 | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:30 seqc.csv | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:42 seqc.csv.1 | |
| -rw-r--r-- 1 vagrant vagrant 8584375694 Oct 3 22:43 SRR950078_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 8650136401 Oct 3 22:28 SRR950078_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9414809474 Oct 3 23:58 SRR950079_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9508216711 Oct 4 00:10 SRR950079_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7845415151 Oct 4 01:08 SRR950080_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7912973223 Oct 4 01:12 SRR950080_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9661234164 Oct 4 02:41 SRR950081_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9758348136 Oct 4 02:36 SRR950081_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5632947596 Oct 4 08:57 SRR950082_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5695733721 Oct 4 08:17 SRR950082_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9673029260 Oct 4 13:46 SRR950083_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 2894010976 Oct 4 15:53 SRR950083_2.fastq.gz | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ ls -al | |
| total 93002556 | |
| drwxr-xr-x 1 vagrant vagrant 680 Oct 4 08:57 . | |
| drwxr-xr-x 1 vagrant vagrant 272 Oct 3 19:42 .. | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html.1 | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 08:17 index.html.2 | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 08:57 index.html.3 | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:30 seqc.csv | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:42 seqc.csv.1 | |
| -rw-r--r-- 1 vagrant vagrant 8584375694 Oct 3 22:43 SRR950078_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 8650136401 Oct 3 22:28 SRR950078_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9414809474 Oct 3 23:58 SRR950079_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9508216711 Oct 4 00:10 SRR950079_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7845415151 Oct 4 01:08 SRR950080_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7912973223 Oct 4 01:12 SRR950080_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9661234164 Oct 4 02:41 SRR950081_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9758348136 Oct 4 02:36 SRR950081_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5632947596 Oct 4 08:57 SRR950082_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5695733721 Oct 4 08:17 SRR950082_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9673029260 Oct 4 13:46 SRR950083_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 2897351512 Oct 4 15:54 SRR950083_2.fastq.gz | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ ls -al | |
| total 93156504 | |
| drwxr-xr-x 1 vagrant vagrant 680 Oct 4 08:57 . | |
| drwxr-xr-x 1 vagrant vagrant 272 Oct 3 19:42 .. | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html.1 | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 08:17 index.html.2 | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 08:57 index.html.3 | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:30 seqc.csv | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:42 seqc.csv.1 | |
| -rw-r--r-- 1 vagrant vagrant 8584375694 Oct 3 22:43 SRR950078_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 8650136401 Oct 3 22:28 SRR950078_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9414809474 Oct 3 23:58 SRR950079_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9508216711 Oct 4 00:10 SRR950079_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7845415151 Oct 4 01:08 SRR950080_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7912973223 Oct 4 01:12 SRR950080_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9661234164 Oct 4 02:41 SRR950081_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9758348136 Oct 4 02:36 SRR950081_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5632947596 Oct 4 08:57 SRR950082_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5695733721 Oct 4 08:17 SRR950082_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9673029260 Oct 4 13:46 SRR950083_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 3054993824 Oct 4 16:49 SRR950083_2.fastq.gz | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ ls -al | |
| total 93504204 | |
| drwxr-xr-x 1 vagrant vagrant 680 Oct 4 08:57 . | |
| drwxr-xr-x 1 vagrant vagrant 272 Oct 3 19:42 .. | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html.1 | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 08:17 index.html.2 | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 08:57 index.html.3 | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:30 seqc.csv | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:42 seqc.csv.1 | |
| -rw-r--r-- 1 vagrant vagrant 8584375694 Oct 3 22:43 SRR950078_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 8650136401 Oct 3 22:28 SRR950078_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9414809474 Oct 3 23:58 SRR950079_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9508216711 Oct 4 00:10 SRR950079_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7845415151 Oct 4 01:08 SRR950080_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7912973223 Oct 4 01:12 SRR950080_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9661234164 Oct 4 02:41 SRR950081_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9758348136 Oct 4 02:36 SRR950081_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5632947596 Oct 4 08:57 SRR950082_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5695733721 Oct 4 08:17 SRR950082_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9673029260 Oct 4 13:46 SRR950083_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 3411041096 Oct 4 18:46 SRR950083_2.fastq.gz | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ ls -al | |
| total 93810140 | |
| drwxr-xr-x 1 vagrant vagrant 680 Oct 4 08:57 . | |
| drwxr-xr-x 1 vagrant vagrant 272 Oct 3 19:42 .. | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html.1 | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 08:17 index.html.2 | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 08:57 index.html.3 | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:30 seqc.csv | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:42 seqc.csv.1 | |
| -rw-r--r-- 1 vagrant vagrant 8584375694 Oct 3 22:43 SRR950078_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 8650136401 Oct 3 22:28 SRR950078_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9414809474 Oct 3 23:58 SRR950079_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9508216711 Oct 4 00:10 SRR950079_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7845415151 Oct 4 01:08 SRR950080_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7912973223 Oct 4 01:12 SRR950080_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9661234164 Oct 4 02:41 SRR950081_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9758348136 Oct 4 02:36 SRR950081_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5632947596 Oct 4 08:57 SRR950082_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5695733721 Oct 4 08:17 SRR950082_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9673029260 Oct 4 13:46 SRR950083_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 3724317344 Oct 4 20:32 SRR950083_2.fastq.gz | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ ls -al | |
| total 95119100 | |
| drwxr-xr-x 1 vagrant vagrant 680 Oct 4 08:57 . | |
| drwxr-xr-x 1 vagrant vagrant 272 Oct 3 19:42 .. | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html.1 | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 08:17 index.html.2 | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 08:57 index.html.3 | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:30 seqc.csv | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:42 seqc.csv.1 | |
| -rw-r--r-- 1 vagrant vagrant 8584375694 Oct 3 22:43 SRR950078_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 8650136401 Oct 3 22:28 SRR950078_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9414809474 Oct 3 23:58 SRR950079_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9508216711 Oct 4 00:10 SRR950079_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7845415151 Oct 4 01:08 SRR950080_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7912973223 Oct 4 01:12 SRR950080_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9661234164 Oct 4 02:41 SRR950081_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9758348136 Oct 4 02:36 SRR950081_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5632947596 Oct 4 08:57 SRR950082_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5695733721 Oct 4 08:17 SRR950082_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9673029260 Oct 4 13:46 SRR950083_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5064693296 Oct 5 05:16 SRR950083_2.fastq.gz | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ ls -al | |
| total 95292544 | |
| drwxr-xr-x 1 vagrant vagrant 680 Oct 4 08:57 . | |
| drwxr-xr-x 1 vagrant vagrant 272 Oct 3 19:42 .. | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html.1 | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 08:17 index.html.2 | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 08:57 index.html.3 | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:30 seqc.csv | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:42 seqc.csv.1 | |
| -rw-r--r-- 1 vagrant vagrant 8584375694 Oct 3 22:43 SRR950078_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 8650136401 Oct 3 22:28 SRR950078_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9414809474 Oct 3 23:58 SRR950079_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9508216711 Oct 4 00:10 SRR950079_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7845415151 Oct 4 01:08 SRR950080_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7912973223 Oct 4 01:12 SRR950080_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9661234164 Oct 4 02:41 SRR950081_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9758348136 Oct 4 02:36 SRR950081_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5632947596 Oct 4 08:57 SRR950082_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5695733721 Oct 4 08:17 SRR950082_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9673029260 Oct 4 13:46 SRR950083_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5242302080 Oct 5 07:16 SRR950083_2.fastq.gz | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ ls -al | |
| total 96596744 | |
| drwxr-xr-x 1 vagrant vagrant 680 Oct 4 08:57 . | |
| drwxr-xr-x 1 vagrant vagrant 272 Oct 3 19:42 .. | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html.1 | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 08:17 index.html.2 | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 08:57 index.html.3 | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:30 seqc.csv | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:42 seqc.csv.1 | |
| -rw-r--r-- 1 vagrant vagrant 8584375694 Oct 3 22:43 SRR950078_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 8650136401 Oct 3 22:28 SRR950078_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9414809474 Oct 3 23:58 SRR950079_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9508216711 Oct 4 00:10 SRR950079_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7845415151 Oct 4 01:08 SRR950080_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7912973223 Oct 4 01:12 SRR950080_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9661234164 Oct 4 02:41 SRR950081_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9758348136 Oct 4 02:36 SRR950081_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5632947596 Oct 4 08:57 SRR950082_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5695733721 Oct 4 08:17 SRR950082_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9673029260 Oct 4 13:46 SRR950083_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 6577799720 Oct 5 15:34 SRR950083_2.fastq.gz | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ ls -al | |
| total 97207264 | |
| drwxr-xr-x 1 vagrant vagrant 680 Oct 4 08:57 . | |
| drwxr-xr-x 1 vagrant vagrant 272 Oct 3 19:42 .. | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 03:20 index.html.1 | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 08:17 index.html.2 | |
| -rw-r--r-- 1 vagrant vagrant 986 Oct 4 08:57 index.html.3 | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:30 seqc.csv | |
| -rw-r--r-- 1 vagrant vagrant 279 Oct 3 19:42 seqc.csv.1 | |
| -rw-r--r-- 1 vagrant vagrant 8584375694 Oct 3 22:43 SRR950078_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 8650136401 Oct 3 22:28 SRR950078_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9414809474 Oct 3 23:58 SRR950079_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9508216711 Oct 4 00:10 SRR950079_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7845415151 Oct 4 01:08 SRR950080_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7912973223 Oct 4 01:12 SRR950080_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9661234164 Oct 4 02:41 SRR950081_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9758348136 Oct 4 02:36 SRR950081_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5632947596 Oct 4 08:57 SRR950082_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 5695733721 Oct 4 08:17 SRR950082_2.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 9673029260 Oct 4 13:46 SRR950083_1.fastq.gz | |
| -rw-r--r-- 1 vagrant vagrant 7202973720 Oct 5 19:05 SRR950083_2.fastq.gz | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ ps | |
| PID TTY TIME CMD | |
| 2362 pts/0 00:00:00 bash | |
| 15308 pts/0 00:00:00 ps | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ ps -auxx | |
| USER PID %CPU %MEM VSZ RSS TTY STAT START TIME COMMAND | |
| root 1 0.0 0.0 33636 2960 ? Ss Oct04 0:01 /sbin/init | |
| root 2 0.0 0.0 0 0 ? S Oct04 0:00 [kthreadd] | |
| root 3 0.0 0.0 0 0 ? S Oct04 0:04 [ksoftirqd/0] | |
| root 4 0.0 0.0 0 0 ? S Oct04 0:00 [kworker/0:0] | |
| root 5 0.0 0.0 0 0 ? S< Oct04 0:00 [kworker/0:0H] | |
| root 7 0.0 0.0 0 0 ? S Oct04 0:08 [rcu_sched] | |
| root 8 0.0 0.0 0 0 ? S Oct04 0:14 [rcuos/0] | |
| root 9 0.0 0.0 0 0 ? S Oct04 0:02 [rcuos/1] | |
| root 10 0.0 0.0 0 0 ? S Oct04 0:05 [rcuos/2] | |
| root 11 0.0 0.0 0 0 ? S Oct04 0:05 [rcuos/3] | |
| root 12 0.0 0.0 0 0 ? S Oct04 0:01 [rcuos/4] | |
| root 13 0.0 0.0 0 0 ? S Oct04 0:01 [rcuos/5] | |
| root 14 0.0 0.0 0 0 ? S Oct04 0:01 [rcuos/6] | |
| root 15 0.0 0.0 0 0 ? S Oct04 0:00 [rcuos/7] | |
| root 16 0.0 0.0 0 0 ? S Oct04 0:00 [rcu_bh] | |
| root 17 0.0 0.0 0 0 ? S Oct04 0:00 [rcuob/0] | |
| root 18 0.0 0.0 0 0 ? S Oct04 0:00 [rcuob/1] | |
| root 19 0.0 0.0 0 0 ? S Oct04 0:00 [rcuob/2] | |
| root 20 0.0 0.0 0 0 ? S Oct04 0:00 [rcuob/3] | |
| root 21 0.0 0.0 0 0 ? S Oct04 0:00 [rcuob/4] | |
| root 22 0.0 0.0 0 0 ? S Oct04 0:00 [rcuob/5] | |
| root 23 0.0 0.0 0 0 ? S Oct04 0:00 [rcuob/6] | |
| root 24 0.0 0.0 0 0 ? S Oct04 0:00 [rcuob/7] | |
| root 25 0.0 0.0 0 0 ? S Oct04 0:00 [migration/0] | |
| root 26 0.0 0.0 0 0 ? S Oct04 0:03 [watchdog/0] | |
| root 27 0.0 0.0 0 0 ? S Oct04 0:05 [watchdog/1] | |
| root 28 0.0 0.0 0 0 ? S Oct04 0:00 [migration/1] | |
| root 29 0.0 0.0 0 0 ? S Oct04 0:00 [ksoftirqd/1] | |
| root 30 0.0 0.0 0 0 ? S Oct04 0:00 [kworker/1:0] | |
| root 31 0.0 0.0 0 0 ? S< Oct04 0:00 [kworker/1:0H] | |
| root 32 0.0 0.0 0 0 ? S Oct04 0:06 [watchdog/2] | |
| root 33 0.0 0.0 0 0 ? S Oct04 0:00 [migration/2] | |
| root 34 0.0 0.0 0 0 ? S Oct04 0:00 [ksoftirqd/2] | |
| root 35 0.0 0.0 0 0 ? S Oct04 0:00 [kworker/2:0] | |
| root 36 0.0 0.0 0 0 ? S< Oct04 0:00 [kworker/2:0H] | |
| root 37 0.0 0.0 0 0 ? S Oct04 0:08 [watchdog/3] | |
| root 38 0.0 0.0 0 0 ? S Oct04 0:00 [migration/3] | |
| root 39 0.0 0.0 0 0 ? S Oct04 0:00 [ksoftirqd/3] | |
| root 40 0.0 0.0 0 0 ? S Oct04 0:00 [kworker/3:0] | |
| root 41 0.0 0.0 0 0 ? S< Oct04 0:00 [kworker/3:0H] | |
| root 42 0.0 0.0 0 0 ? S Oct04 0:09 [watchdog/4] | |
| root 43 0.0 0.0 0 0 ? S Oct04 0:00 [migration/4] | |
| root 44 0.0 0.0 0 0 ? S Oct04 0:00 [ksoftirqd/4] | |
| root 45 0.0 0.0 0 0 ? S Oct04 0:00 [kworker/4:0] | |
| root 46 0.0 0.0 0 0 ? S< Oct04 0:00 [kworker/4:0H] | |
| root 47 0.0 0.0 0 0 ? S Oct04 0:06 [watchdog/5] | |
| root 48 0.0 0.0 0 0 ? S Oct04 0:00 [migration/5] | |
| root 49 0.0 0.0 0 0 ? S Oct04 0:00 [ksoftirqd/5] | |
| root 50 0.0 0.0 0 0 ? S Oct04 0:00 [kworker/5:0] | |
| root 51 0.0 0.0 0 0 ? S< Oct04 0:00 [kworker/5:0H] | |
| root 52 0.0 0.0 0 0 ? S Oct04 0:12 [watchdog/6] | |
| root 53 0.0 0.0 0 0 ? S Oct04 0:00 [migration/6] | |
| root 54 0.0 0.0 0 0 ? S Oct04 0:00 [ksoftirqd/6] | |
| root 55 0.0 0.0 0 0 ? S Oct04 0:00 [kworker/6:0] | |
| root 56 0.0 0.0 0 0 ? S< Oct04 0:00 [kworker/6:0H] | |
| root 57 0.0 0.0 0 0 ? S Oct04 0:12 [watchdog/7] | |
| root 58 0.0 0.0 0 0 ? S Oct04 0:00 [migration/7] | |
| root 59 0.0 0.0 0 0 ? S Oct04 0:00 [ksoftirqd/7] | |
| root 60 0.0 0.0 0 0 ? S Oct04 0:00 [kworker/7:0] | |
| root 61 0.0 0.0 0 0 ? S< Oct04 0:00 [kworker/7:0H] | |
| root 62 0.0 0.0 0 0 ? S< Oct04 0:00 [khelper] | |
| root 63 0.0 0.0 0 0 ? S Oct04 0:00 [kdevtmpfs] | |
| root 64 0.0 0.0 0 0 ? S< Oct04 0:00 [netns] | |
| root 65 0.0 0.0 0 0 ? S< Oct04 0:00 [writeback] | |
| root 66 0.0 0.0 0 0 ? S< Oct04 0:00 [kintegrityd] | |
| root 67 0.0 0.0 0 0 ? S< Oct04 0:00 [bioset] | |
| root 68 0.0 0.0 0 0 ? S< Oct04 0:00 [kworker/u17:0] | |
| root 69 0.0 0.0 0 0 ? S< Oct04 0:00 [kblockd] | |
| root 70 0.0 0.0 0 0 ? S< Oct04 0:00 [ata_sff] | |
| root 71 0.0 0.0 0 0 ? S Oct04 0:00 [khubd] | |
| root 72 0.0 0.0 0 0 ? S< Oct04 0:00 [md] | |
| root 73 0.0 0.0 0 0 ? S< Oct04 0:00 [devfreq_wq] | |
| root 74 0.0 0.0 0 0 ? S Oct04 0:01 [kworker/2:1] | |
| root 75 0.0 0.0 0 0 ? S Oct04 0:00 [khungtaskd] | |
| root 76 0.0 0.0 0 0 ? S Oct04 0:00 [kswapd0] | |
| root 77 0.0 0.0 0 0 ? SN Oct04 0:00 [ksmd] | |
| root 78 0.0 0.0 0 0 ? SN Oct04 0:00 [khugepaged] | |
| root 79 0.0 0.0 0 0 ? S Oct04 0:00 [fsnotify_mark] | |
| root 80 0.0 0.0 0 0 ? S Oct04 0:00 [ecryptfs-kthrea] | |
| root 81 0.0 0.0 0 0 ? S< Oct04 0:00 [crypto] | |
| root 93 0.0 0.0 0 0 ? S< Oct04 0:00 [kthrotld] | |
| root 94 0.0 0.0 0 0 ? S Oct04 0:03 [kworker/1:1] | |
| root 95 0.0 0.0 0 0 ? S Oct04 0:00 [kworker/u16:1] | |
| root 96 0.0 0.0 0 0 ? S Oct04 0:23 [kworker/0:1] | |
| root 115 0.0 0.0 0 0 ? S< Oct04 0:00 [deferwq] | |
| root 116 0.0 0.0 0 0 ? S< Oct04 0:00 [charger_manager] | |
| root 129 0.0 0.0 0 0 ? S Oct04 0:01 [kworker/4:1] | |
| root 163 0.0 0.0 0 0 ? S< Oct04 0:00 [kpsmoused] | |
| root 166 0.0 0.0 0 0 ? S Oct04 0:01 [kworker/7:1] | |
| root 167 0.0 0.0 0 0 ? S Oct04 0:00 [scsi_eh_0] | |
| root 168 0.0 0.0 0 0 ? S Oct04 0:00 [kworker/u16:2] | |
| root 173 0.0 0.0 0 0 ? S Oct04 0:01 [kworker/5:1] | |
| root 174 0.0 0.0 0 0 ? S Oct04 0:01 [kworker/3:1] | |
| root 175 0.0 0.0 0 0 ? S Oct04 0:01 [kworker/6:1] | |
| root 217 0.0 0.0 0 0 ? S Oct04 0:00 [jbd2/sda1-8] | |
| root 218 0.0 0.0 0 0 ? S< Oct04 0:00 [ext4-rsv-conver] | |
| root 435 0.0 0.0 19604 936 ? S Oct04 0:00 upstart-udev-bridge --daemon | |
| root 462 0.0 0.0 50016 1856 ? Ss Oct04 0:00 /lib/systemd/systemd-udevd --daemon | |
| root 526 0.0 0.0 0 0 ? S< Oct04 0:00 [iprt] | |
| root 589 0.0 0.0 15260 628 ? S Oct04 0:00 upstart-socket-bridge --daemon | |
| root 593 0.0 0.0 23420 1104 ? Ss Oct04 0:00 rpcbind | |
| statd 635 0.0 0.0 21544 1380 ? Ss Oct04 0:00 rpc.statd -L | |
| root 666 0.0 0.0 10224 2904 ? Ss Oct04 0:00 dhclient -1 -v -pf /run/dhclient.eth0.pid -lf /var/lib/dhcp/dhclient.eth0.leases eth0 | |
| root 800 0.0 0.0 0 0 ? S< Oct04 0:00 [rpciod] | |
| root 817 0.0 0.0 0 0 ? S< Oct04 0:00 [nfsiod] | |
| root 887 0.0 0.0 25544 436 ? Ss Oct04 0:00 rpc.idmapd | |
| root 902 0.0 0.0 15276 628 ? S Oct04 0:00 upstart-file-bridge --daemon | |
| message+ 942 0.0 0.0 39184 1248 ? Ss Oct04 0:08 dbus-daemon --system --fork | |
| syslog 950 0.0 0.0 257912 1600 ? Ssl Oct04 0:00 rsyslogd | |
| root 966 0.0 0.0 43452 1812 ? Ss Oct04 0:00 /lib/systemd/systemd-logind | |
| root 998 0.0 0.0 14540 960 tty4 Ss+ Oct04 0:00 /sbin/getty -8 38400 tty4 | |
| root 1001 0.0 0.0 14540 956 tty5 Ss+ Oct04 0:00 /sbin/getty -8 38400 tty5 | |
| root 1006 0.0 0.0 14540 952 tty2 Ss+ Oct04 0:00 /sbin/getty -8 38400 tty2 | |
| root 1007 0.0 0.0 14540 952 tty3 Ss+ Oct04 0:00 /sbin/getty -8 38400 tty3 | |
| root 1009 0.0 0.0 14540 952 tty6 Ss+ Oct04 0:00 /sbin/getty -8 38400 tty6 | |
| root 1029 0.0 0.0 61364 3068 ? Ss Oct04 0:00 /usr/sbin/sshd -D | |
| daemon 1035 0.0 0.0 19140 160 ? Ss Oct04 0:00 atd | |
| root 1036 0.0 0.0 23656 932 ? Ss Oct04 0:00 cron | |
| root 1046 0.0 0.0 4368 660 ? Ss Oct04 0:00 acpid -c /etc/acpi/events -s /var/run/acpid.socket | |
| root 1081 0.0 0.0 216612 1068 ? Sl Oct04 0:51 /usr/sbin/VBoxService | |
| root 1096 0.0 0.0 0 0 ? S Oct04 0:00 [kauditd] | |
| root 1684 0.0 0.2 182496 34484 ? Ssl Oct04 0:03 /usr/bin/ruby /usr/bin/puppet agent | |
| root 2278 0.0 0.0 14540 944 tty1 Ss+ Oct04 0:00 /sbin/getty -8 38400 tty1 | |
| root 2308 0.0 0.0 107696 4248 ? Ss Oct04 0:00 sshd: vagrant [priv] | |
| vagrant 2361 0.0 0.0 107696 2184 ? R Oct04 0:00 sshd: vagrant@pts/0 | |
| vagrant 2362 0.0 0.0 23064 5648 pts/0 Ss Oct04 0:00 -bash | |
| root 2394 0.0 0.0 107696 4244 ? Ss Oct04 0:00 sshd: vagrant [priv] | |
| vagrant 2447 0.0 0.0 107696 2184 ? S Oct04 0:00 sshd: vagrant@pts/2 | |
| vagrant 2448 0.0 0.0 23064 5656 pts/2 Ss Oct04 0:00 -bash | |
| vagrant 2662 0.0 0.0 11136 1416 pts/2 S+ Oct04 0:00 bash rnaseq-seqc-getdata.sh | |
| vagrant 2668 0.0 0.0 6200 692 pts/2 S+ Oct04 0:00 xargs -n 1 -P 2 wget -q | |
| vagrant 4831 0.4 0.0 29612 2044 pts/2 S+ Oct04 9:56 wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/SRR950083/SRR950083_2.fastq.gz | |
| root 5143 0.0 0.0 0 0 ? S< Oct04 0:00 [kworker/u17:2] | |
| root 11528 0.0 0.2 114260 34540 ? Sl 06:52 0:00 ruby /usr/bin/chef-client -d -P /var/run/chef/client.pid -c /etc/chef/client.rb -i 1800 -s 20 -L /var/log/ch | |
| vagrant 15309 0.0 0.0 17168 1296 pts/0 R+ 19:05 0:00 ps -auxx | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ kill -9 4831 | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/input$ exit | |
| logout | |
| Connection to 127.0.0.1 closed. | |
| Christophes-Mac-Pro:bcbio pfaucon$ vagrant halt | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| ==> default: Attempting graceful shutdown of VM... | |
| Christophes-Mac-Pro:bcbio pfaucon$ | |
| [Restored] | |
| christophes-pro:bcbio pfaucon$ | |
| [Restored] | |
| christophes-pro:bcbio pfaucon$ vagrant up | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| Bringing machine 'default' up with 'virtualbox' provider... | |
| ==> default: Checking if box 'ubuntu/trusty64' is up to date... | |
| ==> default: VirtualBox VM is already running. | |
| christophes-pro:bcbio pfaucon$ vagrant ssh | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| Welcome to Ubuntu 14.04.1 LTS (GNU/Linux 3.13.0-35-generic x86_64) | |
| * Documentation: https://help.ubuntu.com/ | |
| System information as of Sun Oct 5 20:41:01 UTC 2014 | |
| System load: 0.16 Memory usage: 0% Processes: 105 | |
| Usage of /: 73.9% of 39.34GB Swap usage: 0% Users logged in: 0 | |
| Graph this data and manage this system at: | |
| https://landscape.canonical.com/ | |
| Get cloud support with Ubuntu Advantage Cloud Guest: | |
| http://www.ubuntu.com/business/services/cloud | |
| 11 packages can be updated. | |
| 8 updates are security updates. | |
| Last login: Sat Oct 4 03:18:50 2014 from 10.0.2.2 | |
| vagrant@vagrant-ubuntu-trusty-64:~$ cd /vagrant_data/ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ ls | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ ls | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ pwd | |
| /vagrant_data | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ df -h | |
| Filesystem Size Used Avail Use% Mounted on | |
| /dev/sda1 40G 30G 8.7G 78% / | |
| none 4.0K 0 4.0K 0% /sys/fs/cgroup | |
| udev 7.9G 12K 7.9G 1% /dev | |
| tmpfs 1.6G 332K 1.6G 1% /run | |
| none 5.0M 0 5.0M 0% /run/lock | |
| none 7.9G 0 7.9G 0% /run/shm | |
| none 100M 0 100M 0% /run/user | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ ls /vagrant | |
| vagrant/ vagrant_data/ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ ls /vagrant_data/ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ exit | |
| logout | |
| Connection to 127.0.0.1 closed. | |
| christophes-pro:bcbio pfaucon$ vagrant halt | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| ==> default: Attempting graceful shutdown of VM... | |
| christophes-pro:bcbio pfaucon$ vagrant up | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| Bringing machine 'default' up with 'virtualbox' provider... | |
| ==> default: Checking if box 'ubuntu/trusty64' is up to date... | |
| ==> default: Clearing any previously set forwarded ports... | |
| Vagrant cannot forward the specified ports on this VM, since they | |
| would collide with some other application that is already listening | |
| on these ports. The forwarded port to 8090 is already in use | |
| on the host machine. | |
| To fix this, modify your current projects Vagrantfile to use another | |
| port. Example, where '1234' would be replaced by a unique host port: | |
| config.vm.network :forwarded_port, guest: 8090, host: 1234 | |
| Sometimes, Vagrant will attempt to auto-correct this for you. In this | |
| case, Vagrant was unable to. This is usually because the guest machine | |
| is in a state which doesn't allow modifying port forwarding. | |
| christophes-pro:bcbio pfaucon$ nano Vagrantfile | |
| christophes-pro:bcbio pfaucon$ vagrant halt | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| christophes-pro:bcbio pfaucon$ vagrant up | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| Bringing machine 'default' up with 'virtualbox' provider... | |
| ==> default: Checking if box 'ubuntu/trusty64' is up to date... | |
| ==> default: Clearing any previously set network interfaces... | |
| ==> default: Preparing network interfaces based on configuration... | |
| default: Adapter 1: nat | |
| ==> default: Forwarding ports... | |
| default: 8090 => 8091 (adapter 1) | |
| default: 22 => 2222 (adapter 1) | |
| ==> default: Running 'pre-boot' VM customizations... | |
| ==> default: Booting VM... | |
| ==> default: Waiting for machine to boot. This may take a few minutes... | |
| default: SSH address: 127.0.0.1:2222 | |
| default: SSH username: vagrant | |
| default: SSH auth method: private key | |
| default: Warning: Connection timeout. Retrying... | |
| ==> default: Machine booted and ready! | |
| ==> default: Checking for guest additions in VM... | |
| ==> default: Mounting shared folders... | |
| default: /vagrant => /Volumes/WORK/vagrant/bcbio | |
| default: /vagrant_data => /Volumes/WORK/rnaseq | |
| ==> default: Machine already provisioned. Run `vagrant provision` or use the `--provision` | |
| ==> default: to force provisioning. Provisioners marked to run always will still run. | |
| christophes-pro:bcbio pfaucon$ vagrant ssh | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| Welcome to Ubuntu 14.04.1 LTS (GNU/Linux 3.13.0-35-generic x86_64) | |
| * Documentation: https://help.ubuntu.com/ | |
| System information as of Sun Oct 5 20:45:34 UTC 2014 | |
| System load: 0.44 Processes: 140 | |
| Usage of /: 73.9% of 39.34GB Users logged in: 0 | |
| Memory usage: 1% IP address for eth0: 10.0.2.15 | |
| Swap usage: 0% | |
| Graph this data and manage this system at: | |
| https://landscape.canonical.com/ | |
| Get cloud support with Ubuntu Advantage Cloud Guest: | |
| http://www.ubuntu.com/business/services/cloud | |
| 11 packages can be updated. | |
| 8 updates are security updates. | |
| Last login: Sun Oct 5 20:41:58 2014 from 10.0.2.2 | |
| vagrant@vagrant-ubuntu-trusty-64:~$ ls /vagrant_data | |
| GenomeAnalysisTK-3.2-2.tar.bz2 Miniconda-3.6.0-MacOSX-x86_64.sh rnaseq-seqc-getdata.sh rnaseq-seqc-getdata.sh.bk seqc-test | |
| vagrant@vagrant-ubuntu-trusty-64:~$ cd /vagrant_data/seqc-test/ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test$ ls | |
| input rnaseq-seqc.yaml rnaseq-seqc.yaml.1 rnaseq-seqc.yaml.2 rnaseq-seqc.yaml.3 seqc | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test$ cd .. | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ ls | |
| GenomeAnalysisTK-3.2-2.tar.bz2 Miniconda-3.6.0-MacOSX-x86_64.sh rnaseq-seqc-getdata.sh rnaseq-seqc-getdata.sh.bk seqc-test | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ nano rnaseq-seqc-getdata.sh | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ ls | |
| GenomeAnalysisTK-3.2-2.tar.bz2 Miniconda-3.6.0-MacOSX-x86_64.sh rnaseq-seqc-getdata.sh rnaseq-seqc-getdata.sh.bk seqc-test | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ bash rnaseq-seqc-getdata.sh | |
| --2014-10-05 20:49:10-- https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/examples/rnaseq-seqc.yaml | |
| Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 23.235.47.133 | |
| Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|23.235.47.133|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 307 [text/plain] | |
| Saving to: ‘rnaseq-seqc.yaml’ | |
| 100%[=====================================================================================================================================>] 307 --.-K/s in 0s | |
| 2014-10-05 20:49:15 (2.02 MB/s) - ‘rnaseq-seqc.yaml’ saved [307/307] | |
| --2014-10-05 22:06:46-- https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/examples/seqc.csv | |
| Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 199.27.79.133 | |
| Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|199.27.79.133|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 279 [text/plain] | |
| Saving to: ‘seqc.csv’ | |
| 100%[=====================================================================================================================================>] 279 --.-K/s in 0s | |
| 2014-10-05 22:06:51 (11.5 MB/s) - ‘seqc.csv’ saved [279/279] | |
| description UHRR_rep4 | |
| panel UHRR | |
| description HBRR_rep4 | |
| panel HBRR | |
| description HBRR_rep1 | |
| panel HBRR | |
| description UHRR_rep1 | |
| panel UHRR | |
| description UHRR_rep5 | |
| panel UHRR | |
| description HBRR_rep5 | |
| panel HBRR | |
| description UHRR_rep2 | |
| panel UHRR | |
| description HBRR_rep2 | |
| panel HBRR | |
| description UHRR_rep3 | |
| panel UHRR | |
| description HBRR_rep3 | |
| panel HBRR | |
| Configuration file created at: /vagrant_data/seqc-test/seqc/config/seqc.yaml | |
| Edit to finalize and run with: | |
| cd /vagrant_data/seqc-test/seqc/work | |
| bcbio_nextgen.py ../config/seqc.yaml | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ ls | |
| GenomeAnalysisTK-3.2-2.tar.bz2 Miniconda-3.6.0-MacOSX-x86_64.sh rnaseq-seqc-getdata.sh rnaseq-seqc-getdata.sh.bk seqc-test | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ cd seqc-test/ | |
| input/ seqc/ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ cd seqc-test/seqc/ | |
| config/ work/ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ cd seqc-test/seqc/ | |
| config/ work/ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data$ cd seqc-test/seqc/work/ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ ls | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ bcbio_nextgen.py ../config/seqc.yaml -n 8 | |
| [2014-10-05 22:47] Using input YAML configuration: /vagrant_data/seqc-test/seqc/config/seqc.yaml | |
| [2014-10-05 22:47] Checking sample YAML configuration: /vagrant_data/seqc-test/seqc/config/seqc.yaml | |
| [2014-10-05 22:47] Testing minimum versions of installed programs | |
| [2014-10-05 22:47] Resource requests: AlienTrimmer, picard; memory: 2.0, 3.5; cores: 1, 1 | |
| [2014-10-05 22:47] Configuring 4 jobs to run, using 1 cores each with 3.8g of memory reserved for each job | |
| [2014-10-05 22:47] Timing: adapter trimming | |
| [2014-10-05 22:47] multiprocessing: prepare_sample | |
| [2014-10-05 22:47] Preparing UHRR_rep1 | |
| [2014-10-05 22:47] Preparing HBRR_rep1 | |
| [2014-10-05 22:47] Preparing UHRR_rep2 | |
| [2014-10-05 22:47] Preparing HBRR_rep2 | |
| [2014-10-05 22:47] Preparing UHRR_rep3 | |
| [2014-10-05 22:47] Preparing HBRR_rep3 | |
| [2014-10-05 22:47] multiprocessing: trim_sample | |
| [2014-10-05 22:47] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950078_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950078_2.fastq.gz. | |
| [2014-10-05 22:47] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950079_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950079_2.fastq.gz. | |
| [2014-10-05 22:47] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950080_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950080_2.fastq.gz. | |
| [2014-10-05 22:47] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950081_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950081_2.fastq.gz. | |
| [2014-10-05 22:47] Trimming /vagrant_data/seqc-test/input/SRR950080_1.fastq.gz and /vagrant_data/seqc-test/input/SRR950080_2.fastq.gz in single end mode with cutadapt. | |
| [2014-10-05 22:47] Trimming /vagrant_data/seqc-test/input/SRR950081_1.fastq.gz and /vagrant_data/seqc-test/input/SRR950081_2.fastq.gz in single end mode with cutadapt. | |
| [2014-10-05 22:47] Trimming /vagrant_data/seqc-test/input/SRR950079_1.fastq.gz and /vagrant_data/seqc-test/input/SRR950079_2.fastq.gz in single end mode with cutadapt. | |
| [2014-10-05 22:47] Trimming /vagrant_data/seqc-test/input/SRR950078_1.fastq.gz and /vagrant_data/seqc-test/input/SRR950078_2.fastq.gz in single end mode with cutadapt. | |
| ^C[2014-10-05 22:47] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 78, in _do_run | |
| line = s.stdout.readline() | |
| KeyboardInterrupt | |
| [2014-10-05 22:47] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 78, in _do_run | |
| line = s.stdout.readline() | |
| KeyboardInterrupt | |
| [2014-10-05 22:47] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 78, in _do_run | |
| line = s.stdout.readline() | |
| KeyboardInterrupt | |
| [2014-10-05 22:47] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 78, in _do_run | |
| line = s.stdout.readline() | |
| KeyboardInterrupt | |
| [2014-10-05 22:47] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950082_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950082_2.fastq.gz. | |
| [2014-10-05 22:47] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950083_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950083_2.fastq.gz. | |
| Traceback (most recent call last): | |
| File "/usr/local/bin/bcbio_nextgen.py", line 216, in <module> | |
| main(**kwargs) | |
| File "/usr/local/bin/bcbio_nextgen.py", line 42, in main | |
| run_main(**kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 36, in run_main | |
| fc_dir, run_info_yaml) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 82, in _run_toplevel | |
| for xs in pipeline.run(config, config_file, parallel, dirs, pipeline_items): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 299, in run | |
| samples = run_parallel("trim_sample", samples) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel | |
| return run_multicore(fn, items, config, parallel=parallel) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 84, in run_multicore | |
| for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 660, in __call__ | |
| self.retrieve() | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 526, in retrieve | |
| raise exception | |
| KeyboardInterrupt | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ clear | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ bcbio_nextgen.py ../config/seqc.yaml -n 8 | |
| [2014-10-05 22:47] Using input YAML configuration: /vagrant_data/seqc-test/seqc/config/seqc.yaml | |
| [2014-10-05 22:47] Checking sample YAML configuration: /vagrant_data/seqc-test/seqc/config/seqc.yaml | |
| [2014-10-05 22:47] Testing minimum versions of installed programs | |
| [2014-10-05 22:47] Resource requests: AlienTrimmer, picard; memory: 2.0, 3.5; cores: 1, 1 | |
| [2014-10-05 22:47] Configuring 4 jobs to run, using 1 cores each with 3.8g of memory reserved for each job | |
| [2014-10-05 22:47] Timing: adapter trimming | |
| [2014-10-05 22:47] multiprocessing: prepare_sample | |
| [2014-10-05 22:47] Preparing HBRR_rep1 | |
| [2014-10-05 22:47] Preparing HBRR_rep2 | |
| [2014-10-05 22:47] Preparing UHRR_rep2 | |
| [2014-10-05 22:47] Preparing UHRR_rep1 | |
| [2014-10-05 22:47] Preparing UHRR_rep3 | |
| [2014-10-05 22:47] Preparing HBRR_rep3 | |
| [2014-10-05 22:47] multiprocessing: trim_sample | |
| [2014-10-05 22:47] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950079_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950079_2.fastq.gz. | |
| [2014-10-05 22:47] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950078_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950078_2.fastq.gz. | |
| [2014-10-05 22:47] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950080_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950080_2.fastq.gz. | |
| [2014-10-05 22:47] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950081_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950081_2.fastq.gz. | |
| [2014-10-05 22:47] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950083_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950083_2.fastq.gz. | |
| [2014-10-05 22:47] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950082_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950082_2.fastq.gz. | |
| [2014-10-05 22:47] Trimming /vagrant_data/seqc-test/input/SRR950083_1.fastq.gz and /vagrant_data/seqc-test/input/SRR950083_2.fastq.gz in single end mode with cutadapt. | |
| [2014-10-05 22:47] Trimming /vagrant_data/seqc-test/input/SRR950082_1.fastq.gz and /vagrant_data/seqc-test/input/SRR950082_2.fastq.gz in single end mode with cutadapt. | |
| [2014-10-05 23:55] cutadapt version 1.4.2 | |
| [2014-10-05 23:55] Command line parameters: --times=2 --quality-base=33 --quality-cutoff=5 --format=fastq --adapter=AAAAAAAAAAAAA --adapter=TTTTTTTTTTTTT --adapter=AGATCGGAAGAG --adapter=CTCTTCCGATCT --minimum-length=25 -o /vagrant_data/seqc-test/seqc/work/trimmed/SRR950082_1.trimmed.tmp.fastq.gz -p /vagrant_data/seqc-test/seqc/work/trimmed/SRR950082_2.trimmed.tmp.fastq.gz /vagrant_data/seqc-test/input/SRR950082_1.fastq.gz /vagrant_data/seqc-test/input/SRR950082_2.fastq.gz | |
| [2014-10-05 23:55] Maximum error rate: 10.00% | |
| [2014-10-05 23:55] No. of adapters: 4 | |
| [2014-10-05 23:55] Processed reads: 67207757 | |
| [2014-10-05 23:55] Processed bases: 6787983457 bp (6788.0 Mbp) | |
| [2014-10-05 23:55] Trimmed reads: 13820415 (20.6%) | |
| [2014-10-05 23:55] Quality-trimmed: 851318208 bp (851.3 Mbp) (12.54% of total) | |
| [2014-10-05 23:55] Trimmed bases: 816360055 bp (816.4 Mbp) (12.03% of total) | |
| [2014-10-05 23:55] Too short reads: 9432645 (14.0% of processed reads) | |
| [2014-10-05 23:55] Too long reads: 0 (0.0% of processed reads) | |
| [2014-10-05 23:55] Total time: 3864.51 s | |
| [2014-10-05 23:55] Time per read: 0.058 ms | |
| [2014-10-05 23:55] | |
| [2014-10-05 23:55] === Adapter 1 === | |
| [2014-10-05 23:55] | |
| [2014-10-05 23:55] Adapter 'AAAAAAAAAAAAA', length 13, was trimmed 4581151 times. | |
| [2014-10-05 23:55] | |
| [2014-10-05 23:55] No. of allowed errors: | |
| [2014-10-05 23:55] 0-9 bp: 0; 10-13 bp: 1 | |
| [2014-10-05 23:55] | |
| [2014-10-05 23:55] Overview of removed sequences | |
| [2014-10-05 23:55] length count expect max.err error counts | |
| [2014-10-05 23:55] 3 2174294 1050121.2 0 2174294 | |
| [2014-10-05 23:55] 4 794746 262530.3 0 794746 | |
| [2014-10-05 23:55] 5 338811 65632.6 0 338811 | |
| [2014-10-05 23:55] 6 155101 16408.1 0 155101 | |
| [2014-10-05 23:55] 7 86785 4102.0 0 86785 | |
| [2014-10-05 23:55] 8 75446 1025.5 0 75446 | |
| [2014-10-05 23:55] 9 55617 256.4 0 55617 | |
| [2014-10-05 23:55] 10 76781 64.1 1 35969 40812 | |
| [2014-10-05 23:55] 11 58190 16.0 1 32676 25514 | |
| [2014-10-05 23:55] 12 43652 4.0 1 26478 17174 | |
| [2014-10-05 23:55] 13 38389 1.0 1 25768 12621 | |
| [2014-10-05 23:55] 14 38056 1.0 1 27551 10505 | |
| [2014-10-05 23:55] 15 35545 1.0 1 25943 9602 | |
| [2014-10-05 23:55] 16 31238 1.0 1 22828 8410 | |
| [2014-10-05 23:55] 17 26867 1.0 1 19488 7379 | |
| [2014-10-05 23:55] 18 23433 1.0 1 16866 6567 | |
| [2014-10-05 23:55] 19 20777 1.0 1 14923 5854 | |
| [2014-10-05 23:55] 20 18484 1.0 1 12849 5635 | |
| [2014-10-05 23:55] 21 17475 1.0 1 11680 5795 | |
| [2014-10-05 23:55] 22 16074 1.0 1 10578 5496 | |
| [2014-10-05 23:55] 23 14892 1.0 1 9498 5394 | |
| [2014-10-05 23:55] 24 14301 1.0 1 8865 5436 | |
| [2014-10-05 23:55] 25 13131 1.0 1 7932 5199 | |
| [2014-10-05 23:55] 26 12245 1.0 1 7112 5133 | |
| [2014-10-05 23:55] 27 11376 1.0 1 6121 5255 | |
| [2014-10-05 23:55] 28 10532 1.0 1 5528 5004 | |
| [2014-10-05 23:55] 29 10311 1.0 1 5084 5227 | |
| [2014-10-05 23:55] 30 9924 1.0 1 4787 5137 | |
| [2014-10-05 23:55] 31 9119 1.0 1 4409 4710 | |
| [2014-10-05 23:55] 32 8786 1.0 1 4069 4717 | |
| [2014-10-05 23:55] 33 8923 1.0 1 4268 4655 | |
| [2014-10-05 23:55] 34 8523 1.0 1 3970 4553 | |
| [2014-10-05 23:55] 35 8114 1.0 1 3754 4360 | |
| [2014-10-05 23:55] 36 7499 1.0 1 3318 4181 | |
| [2014-10-05 23:55] 37 7115 1.0 1 2935 4180 | |
| [2014-10-05 23:55] 38 8991 1.0 1 3209 5782 | |
| [2014-10-05 23:55] 39 7216 1.0 1 2610 4606 | |
| [2014-10-05 23:55] 40 6728 1.0 1 2879 3849 | |
| [2014-10-05 23:55] 41 6194 1.0 1 2452 3742 | |
| [2014-10-05 23:55] 42 6277 1.0 1 2718 3559 | |
| [2014-10-05 23:55] 43 6426 1.0 1 2767 3659 | |
| [2014-10-05 23:55] 44 6621 1.0 1 2709 3912 | |
| [2014-10-05 23:55] 45 6359 1.0 1 2692 3667 | |
| [2014-10-05 23:55] 46 5649 1.0 1 2037 3612 | |
| [2014-10-05 23:55] 47 5448 1.0 1 1804 3644 | |
| [2014-10-05 23:55] 48 5693 1.0 1 1720 3973 | |
| [2014-10-05 23:55] 49 5147 1.0 1 1578 3569 | |
| [2014-10-05 23:55] 50 4971 1.0 1 1472 3499 | |
| [2014-10-05 23:55] 51 4826 1.0 1 1343 3483 | |
| [2014-10-05 23:55] 52 4848 1.0 1 1408 3440 | |
| [2014-10-05 23:55] 53 4903 1.0 1 1339 3564 | |
| [2014-10-05 23:55] 54 5047 1.0 1 1366 3681 | |
| [2014-10-05 23:55] 55 4968 1.0 1 1381 3587 | |
| [2014-10-05 23:55] 56 4857 1.0 1 1420 3437 | |
| [2014-10-05 23:55] 57 5103 1.0 1 1262 3841 | |
| [2014-10-05 23:55] 58 4845 1.0 1 1238 3607 | |
| [2014-10-05 23:55] 59 4994 1.0 1 1307 3687 | |
| [2014-10-05 23:55] 60 4563 1.0 1 1131 3432 | |
| [2014-10-05 23:55] 61 4822 1.0 1 1298 3524 | |
| [2014-10-05 23:55] 62 4615 1.0 1 1223 3392 | |
| [2014-10-05 23:55] 63 4545 1.0 1 1172 3373 | |
| [2014-10-05 23:55] 64 4606 1.0 1 1149 3457 | |
| [2014-10-05 23:55] 65 4584 1.0 1 1218 3366 | |
| [2014-10-05 23:55] 66 4650 1.0 1 1235 3415 | |
| [2014-10-05 23:55] 67 4613 1.0 1 1191 3422 | |
| [2014-10-05 23:55] 68 4588 1.0 1 1244 3344 | |
| [2014-10-05 23:55] 69 4551 1.0 1 1077 3474 | |
| [2014-10-05 23:55] 70 4526 1.0 1 977 3549 | |
| [2014-10-05 23:55] 71 4722 1.0 1 1139 3583 | |
| [2014-10-05 23:55] 72 4559 1.0 1 1063 3496 | |
| [2014-10-05 23:55] 73 4572 1.0 1 950 3622 | |
| [2014-10-05 23:55] 74 4711 1.0 1 1096 3615 | |
| [2014-10-05 23:55] 75 4199 1.0 1 961 3238 | |
| [2014-10-05 23:55] 76 4719 1.0 1 1008 3711 | |
| [2014-10-05 23:55] 77 4259 1.0 1 923 3336 | |
| [2014-10-05 23:55] 78 4336 1.0 1 1004 3332 | |
| [2014-10-05 23:55] 79 4140 1.0 1 922 3218 | |
| [2014-10-05 23:55] 80 4350 1.0 1 896 3454 | |
| [2014-10-05 23:55] 81 3988 1.0 1 763 3225 | |
| [2014-10-05 23:55] 82 4269 1.0 1 766 3503 | |
| [2014-10-05 23:55] 83 4067 1.0 1 803 3264 | |
| [2014-10-05 23:55] 84 4059 1.0 1 881 3178 | |
| [2014-10-05 23:55] 85 3950 1.0 1 888 3062 | |
| [2014-10-05 23:55] 86 3910 1.0 1 960 2950 | |
| [2014-10-05 23:55] 87 4002 1.0 1 855 3147 | |
| [2014-10-05 23:55] 88 3795 1.0 1 771 3024 | |
| [2014-10-05 23:55] 89 3770 1.0 1 676 3094 | |
| [2014-10-05 23:55] 90 3245 1.0 1 617 2628 | |
| [2014-10-05 23:55] 91 2909 1.0 1 632 2277 | |
| [2014-10-05 23:55] 92 4809 1.0 1 881 3928 | |
| [2014-10-05 23:55] 93 5043 1.0 1 776 4267 | |
| [2014-10-05 23:55] 94 4700 1.0 1 674 4026 | |
| [2014-10-05 23:55] 95 2606 1.0 1 380 2226 | |
| [2014-10-05 23:55] 96 2119 1.0 1 334 1785 | |
| [2014-10-05 23:55] 97 2411 1.0 1 393 2018 | |
| [2014-10-05 23:55] 98 2408 1.0 1 351 2057 | |
| [2014-10-05 23:55] 99 2132 1.0 1 326 1806 | |
| [2014-10-05 23:55] 100 3770 1.0 1 422 3348 | |
| [2014-10-05 23:55] 101 7296 1.0 1 870 6426 | |
| [2014-10-05 23:55] | |
| [2014-10-05 23:55] === Adapter 2 === | |
| [2014-10-05 23:55] | |
| [2014-10-05 23:55] Adapter 'TTTTTTTTTTTTT', length 13, was trimmed 4295973 times. | |
| [2014-10-05 23:55] | |
| [2014-10-05 23:55] No. of allowed errors: | |
| [2014-10-05 23:55] 0-9 bp: 0; 10-13 bp: 1 | |
| [2014-10-05 23:55] | |
| [2014-10-05 23:55] Overview of removed sequences | |
| [2014-10-05 23:55] length count expect max.err error counts | |
| [2014-10-05 23:55] 3 2106517 1050121.2 0 2106517 | |
| [2014-10-05 23:55] 4 756974 262530.3 0 756974 | |
| [2014-10-05 23:55] 5 287418 65632.6 0 287418 | |
| [2014-10-05 23:55] 6 98272 16408.1 0 98272 | |
| [2014-10-05 23:55] 7 60034 4102.0 0 60034 | |
| [2014-10-05 23:55] 8 23611 1025.5 0 23611 | |
| [2014-10-05 23:55] 9 18276 256.4 0 18276 | |
| [2014-10-05 23:55] 10 55739 64.1 1 15908 39831 | |
| [2014-10-05 23:55] 11 41712 16.0 1 15401 26311 | |
| [2014-10-05 23:55] 12 43950 4.0 1 26377 17573 | |
| [2014-10-05 23:55] 13 41455 1.0 1 29406 12049 | |
| [2014-10-05 23:55] 14 44097 1.0 1 34022 10075 | |
| [2014-10-05 23:55] 15 44851 1.0 1 36514 8337 | |
| [2014-10-05 23:55] 16 42416 1.0 1 35329 7087 | |
| [2014-10-05 23:55] 17 40361 1.0 1 33759 6602 | |
| [2014-10-05 23:55] 18 32337 1.0 1 26064 6273 | |
| [2014-10-05 23:55] 19 26059 1.0 1 19998 6061 | |
| [2014-10-05 23:55] 20 26976 1.0 1 17518 9458 | |
| [2014-10-05 23:55] 21 22040 1.0 1 16121 5919 | |
| [2014-10-05 23:55] 22 19245 1.0 1 13777 5468 | |
| [2014-10-05 23:55] 23 17566 1.0 1 12218 5348 | |
| [2014-10-05 23:55] 24 16842 1.0 1 10806 6036 | |
| [2014-10-05 23:55] 25 15064 1.0 1 9259 5805 | |
| [2014-10-05 23:55] 26 12979 1.0 1 7819 5160 | |
| [2014-10-05 23:55] 27 11698 1.0 1 6941 4757 | |
| [2014-10-05 23:55] 28 11304 1.0 1 6076 5228 | |
| [2014-10-05 23:55] 29 10417 1.0 1 5340 5077 | |
| [2014-10-05 23:55] 30 9229 1.0 1 4675 4554 | |
| [2014-10-05 23:55] 31 8522 1.0 1 4057 4465 | |
| [2014-10-05 23:55] 32 8340 1.0 1 3746 4594 | |
| [2014-10-05 23:55] 33 7909 1.0 1 3365 4544 | |
| [2014-10-05 23:55] 34 7276 1.0 1 2849 4427 | |
| [2014-10-05 23:55] 35 6815 1.0 1 2632 4183 | |
| [2014-10-05 23:55] 36 6550 1.0 1 2412 4138 | |
| [2014-10-05 23:55] 37 6426 1.0 1 2325 4101 | |
| [2014-10-05 23:55] 38 6432 1.0 1 2158 4274 | |
| [2014-10-05 23:55] 39 6551 1.0 1 2202 4349 | |
| [2014-10-05 23:55] 40 6497 1.0 1 2012 4485 | |
| [2014-10-05 23:55] 41 6353 1.0 1 2072 4281 | |
| [2014-10-05 23:55] 42 6464 1.0 1 2071 4393 | |
| [2014-10-05 23:55] 43 6538 1.0 1 2049 4489 | |
| [2014-10-05 23:55] 44 6029 1.0 1 1959 4070 | |
| [2014-10-05 23:55] 45 6341 1.0 1 2032 4309 | |
| [2014-10-05 23:55] 46 5895 1.0 1 1817 4078 | |
| [2014-10-05 23:55] 47 5947 1.0 1 1755 4192 | |
| [2014-10-05 23:55] 48 5999 1.0 1 1666 4333 | |
| [2014-10-05 23:55] 49 6042 1.0 1 1499 4543 | |
| [2014-10-05 23:55] 50 5636 1.0 1 1460 4176 | |
| [2014-10-05 23:55] 51 5033 1.0 1 1371 3662 | |
| [2014-10-05 23:55] 52 5095 1.0 1 1317 3778 | |
| [2014-10-05 23:55] 53 4688 1.0 1 1210 3478 | |
| [2014-10-05 23:55] 54 4837 1.0 1 1205 3632 | |
| [2014-10-05 23:55] 55 5095 1.0 1 1321 3774 | |
| [2014-10-05 23:55] 56 5010 1.0 1 1390 3620 | |
| [2014-10-05 23:55] 57 4783 1.0 1 1180 3603 | |
| [2014-10-05 23:55] 58 4697 1.0 1 1081 3616 | |
| [2014-10-05 23:55] 59 4976 1.0 1 1063 3913 | |
| [2014-10-05 23:55] 60 4501 1.0 1 976 3525 | |
| [2014-10-05 23:55] 61 4707 1.0 1 1046 3661 | |
| [2014-10-05 23:55] 62 4690 1.0 1 1053 3637 | |
| [2014-10-05 23:55] 63 4361 1.0 1 969 3392 | |
| [2014-10-05 23:55] 64 4528 1.0 1 961 3567 | |
| [2014-10-05 23:55] 65 4406 1.0 1 918 3488 | |
| [2014-10-05 23:55] 66 4473 1.0 1 894 3579 | |
| [2014-10-05 23:55] 67 4531 1.0 1 928 3603 | |
| [2014-10-05 23:55] 68 4456 1.0 1 868 3588 | |
| [2014-10-05 23:55] 69 4378 1.0 1 907 3471 | |
| [2014-10-05 23:55] 70 4623 1.0 1 871 3752 | |
| [2014-10-05 23:55] 71 4364 1.0 1 897 3467 | |
| [2014-10-05 23:55] 72 4493 1.0 1 928 3565 | |
| [2014-10-05 23:55] 73 4207 1.0 1 868 3339 | |
| [2014-10-05 23:55] 74 4009 1.0 1 765 3244 | |
| [2014-10-05 23:55] 75 3843 1.0 1 719 3124 | |
| [2014-10-05 23:55] 76 4248 1.0 1 760 3488 | |
| [2014-10-05 23:55] 77 4352 1.0 1 738 3614 | |
| [2014-10-05 23:55] 78 4017 1.0 1 768 3249 | |
| [2014-10-05 23:55] 79 4026 1.0 1 737 3289 | |
| [2014-10-05 23:55] 80 4092 1.0 1 706 3386 | |
| [2014-10-05 23:55] 81 4251 1.0 1 752 3499 | |
| [2014-10-05 23:55] 82 4251 1.0 1 698 3553 | |
| [2014-10-05 23:55] 83 3988 1.0 1 725 3263 | |
| [2014-10-05 23:55] 84 3806 1.0 1 592 3214 | |
| [2014-10-05 23:55] 85 3834 1.0 1 623 3211 | |
| [2014-10-05 23:55] 86 3930 1.0 1 645 3285 | |
| [2014-10-05 23:55] 87 3649 1.0 1 588 3061 | |
| [2014-10-05 23:55] 88 4014 1.0 1 600 3414 | |
| [2014-10-05 23:55] 89 3975 1.0 1 692 3283 | |
| [2014-10-05 23:55] 90 5433 1.0 1 780 4653 | |
| [2014-10-05 23:55] 91 4588 1.0 1 668 3920 | |
| [2014-10-05 23:55] 92 4547 1.0 1 608 3939 | |
| [2014-10-05 23:55] 93 3963 1.0 1 688 3275 | |
| [2014-10-05 23:55] 94 2714 1.0 1 498 2216 | |
| [2014-10-05 23:55] 95 3502 1.0 1 507 2995 | |
| [2014-10-05 23:55] 96 3324 1.0 1 482 2842 | |
| [2014-10-05 23:55] 97 3482 1.0 1 404 3078 | |
| [2014-10-05 23:55] 98 2440 1.0 1 444 1996 | |
| [2014-10-05 23:55] 99 2114 1.0 1 324 1790 | |
| [2014-10-05 23:55] 100 7556 1.0 1 562 6994 | |
| [2014-10-05 23:55] 101 11092 1.0 1 2476 8616 | |
| [2014-10-05 23:55] | |
| [2014-10-05 23:55] === Adapter 3 === | |
| [2014-10-05 23:55] | |
| [2014-10-05 23:55] Adapter 'AGATCGGAAGAG', length 12, was trimmed 15478695 times. | |
| [2014-10-05 23:55] | |
| [2014-10-05 23:55] No. of allowed errors: | |
| [2014-10-05 23:55] 0-9 bp: 0; 10-12 bp: 1 | |
| [2014-10-05 23:55] | |
| [2014-10-05 23:55] Overview of removed sequences | |
| [2014-10-05 23:55] length count expect max.err error counts | |
| [2014-10-05 23:55] 3 2521590 1050121.2 0 2521590 | |
| [2014-10-05 23:55] 4 692633 262530.3 0 692633 | |
| [2014-10-05 23:55] 5 292187 65632.6 0 292187 | |
| [2014-10-05 23:55] 6 260396 16408.1 0 260396 | |
| [2014-10-05 23:55] 7 180324 4102.0 0 180324 | |
| [2014-10-05 23:55] 8 211228 1025.5 0 211228 | |
| [2014-10-05 23:55] 9 180491 256.4 0 172280 8211 | |
| [2014-10-05 23:55] 10 137060 64.1 1 125134 11926 | |
| [2014-10-05 23:55] 11 112006 16.0 1 102087 9919 | |
| [2014-10-05 23:55] 12 105580 4.0 1 98494 7086 | |
| [2014-10-05 23:55] 13 83432 4.0 1 76327 7105 | |
| [2014-10-05 23:55] 14 77147 4.0 1 70784 6363 | |
| [2014-10-05 23:55] 15 76271 4.0 1 69035 7236 | |
| [2014-10-05 23:55] 16 72678 4.0 1 64651 8027 | |
| [2014-10-05 23:55] 17 75964 4.0 1 68310 7654 | |
| [2014-10-05 23:55] 18 66982 4.0 1 61637 5345 | |
| [2014-10-05 23:55] 19 46184 4.0 1 41193 4991 | |
| [2014-10-05 23:55] 20 45738 4.0 1 40076 5662 | |
| [2014-10-05 23:55] 21 37969 4.0 1 32207 5762 | |
| [2014-10-05 23:55] 22 41950 4.0 1 26061 15889 | |
| [2014-10-05 23:55] 23 34299 4.0 1 26151 8148 | |
| [2014-10-05 23:55] 24 26471 4.0 1 21328 5143 | |
| [2014-10-05 23:55] 25 26755 4.0 1 21749 5006 | |
| [2014-10-05 23:55] 26 23960 4.0 1 16554 7406 | |
| [2014-10-05 23:55] 27 40688 4.0 1 21887 18801 | |
| [2014-10-05 23:55] 28 32221 4.0 1 20862 11359 | |
| [2014-10-05 23:55] 29 32689 4.0 1 19544 13145 | |
| [2014-10-05 23:55] 30 28788 4.0 1 19415 9373 | |
| [2014-10-05 23:55] 31 20911 4.0 1 10991 9920 | |
| [2014-10-05 23:55] 32 21923 4.0 1 10533 11390 | |
| [2014-10-05 23:55] 33 34313 4.0 1 9448 24865 | |
| [2014-10-05 23:55] 34 32979 4.0 1 12382 20597 | |
| [2014-10-05 23:55] 35 30267 4.0 1 10089 20178 | |
| [2014-10-05 23:55] 36 31692 4.0 1 11262 20430 | |
| [2014-10-05 23:55] 37 37286 4.0 1 9245 28041 | |
| [2014-10-05 23:55] 38 39887 4.0 1 12250 27637 | |
| [2014-10-05 23:55] 39 42180 4.0 1 10278 31902 | |
| [2014-10-05 23:55] 40 52671 4.0 1 12351 40320 | |
| [2014-10-05 23:55] 41 31973 4.0 1 15147 16826 | |
| [2014-10-05 23:55] 42 18596 4.0 1 9036 9560 | |
| [2014-10-05 23:55] 43 14407 4.0 1 5209 9198 | |
| [2014-10-05 23:55] 44 22627 4.0 1 4151 18476 | |
| [2014-10-05 23:55] 45 24934 4.0 1 5579 19355 | |
| [2014-10-05 23:55] 46 18157 4.0 1 6917 11240 | |
| [2014-10-05 23:55] 47 18505 4.0 1 3891 14614 | |
| [2014-10-05 23:55] 48 17590 4.0 1 4642 12948 | |
| [2014-10-05 23:55] 49 14082 4.0 1 4695 9387 | |
| [2014-10-05 23:55] 50 21788 4.0 1 6754 15034 | |
| [2014-10-05 23:55] 51 30074 4.0 1 5128 24946 | |
| [2014-10-05 23:55] 52 36855 4.0 1 7295 29560 | |
| [2014-10-05 23:55] 53 15955 4.0 1 6361 9594 | |
| [2014-10-05 23:55] 54 12676 4.0 1 2550 10126 | |
| [2014-10-05 23:55] 55 20732 4.0 1 2951 17781 | |
| [2014-10-05 23:55] 56 26783 4.0 1 4492 22291 | |
| [2014-10-05 23:55] 57 32590 4.0 1 4322 28268 | |
| [2014-10-05 23:55] 58 44122 4.0 1 5438 38684 | |
| [2014-10-05 23:55] 59 39220 4.0 1 6660 32560 | |
| [2014-10-05 23:55] 60 49769 4.0 1 5800 43969 | |
| [2014-10-05 23:55] 61 69369 4.0 1 6436 62933 | |
| [2014-10-05 23:55] 62 165310 4.0 1 10764 154546 | |
| [2014-10-05 23:55] 63 289487 4.0 1 19880 269607 | |
| [2014-10-05 23:55] 64 153928 4.0 1 34044 119884 | |
| [2014-10-05 23:55] 65 141005 4.0 1 17108 123897 | |
| [2014-10-05 23:55] 66 260065 4.0 1 17936 242129 | |
| [2014-10-05 23:55] 67 428074 4.0 1 31901 396173 | |
| [2014-10-05 23:55] 68 822531 4.0 1 53898 768633 | |
| [2014-10-05 23:55] 69 1523562 4.0 1 97565 1425997 | |
| [2014-10-05 23:55] 70 1340335 4.0 1 182388 1157947 | |
| [2014-10-05 23:55] 71 1504613 4.0 1 136225 1368388 | |
| [2014-10-05 23:55] 72 1370364 4.0 1 156212 1214152 | |
| [2014-10-05 23:55] 73 670262 4.0 1 136009 534253 | |
| [2014-10-05 23:55] 74 67735 4.0 1 53016 14719 | |
| [2014-10-05 23:55] 75 5480 4.0 1 3900 1580 | |
| [2014-10-05 23:55] 76 3425 4.0 1 1161 2264 | |
| [2014-10-05 23:55] 77 3043 4.0 1 365 2678 | |
| [2014-10-05 23:55] 78 3151 4.0 1 363 2788 | |
| [2014-10-05 23:55] 79 3217 4.0 1 327 2890 | |
| [2014-10-05 23:55] 80 3942 4.0 1 434 3508 | |
| [2014-10-05 23:55] 81 3793 4.0 1 415 3378 | |
| [2014-10-05 23:55] 82 3657 4.0 1 425 3232 | |
| [2014-10-05 23:55] 83 3981 4.0 1 399 3582 | |
| [2014-10-05 23:55] 84 4307 4.0 1 418 3889 | |
| [2014-10-05 23:55] 85 4349 4.0 1 493 3856 | |
| [2014-10-05 23:55] 86 4633 4.0 1 466 4167 | |
| [2014-10-05 23:55] 87 5405 4.0 1 634 4771 | |
| [2014-10-05 23:55] 88 6146 4.0 1 617 5529 | |
| [2014-10-05 23:55] 89 6274 4.0 1 756 5518 | |
| [2014-10-05 23:55] 90 7502 4.0 1 755 6747 | |
| [2014-10-05 23:55] 91 7737 4.0 1 915 6822 | |
| [2014-10-05 23:55] 92 8944 4.0 1 770 8174 | |
| [2014-10-05 23:55] 93 10150 4.0 1 964 9186 | |
| [2014-10-05 23:55] 94 8654 4.0 1 1262 7392 | |
| [2014-10-05 23:55] 95 8202 4.0 1 891 7311 | |
| [2014-10-05 23:55] 96 9759 4.0 1 1060 8699 | |
| [2014-10-05 23:55] 97 12012 4.0 1 1244 10768 | |
| [2014-10-05 23:55] 98 10133 4.0 1 1598 8535 | |
| [2014-10-05 23:55] 99 8588 4.0 1 834 7754 | |
| [2014-10-05 23:55] 100 6392 4.0 1 982 5410 | |
| [2014-10-05 23:55] 101 89954 4.0 1 18432 71522 | |
| [2014-10-05 23:55] | |
| [2014-10-05 23:55] === Adapter 4 === | |
| [2014-10-05 23:55] | |
| [2014-10-05 23:55] Adapter 'CTCTTCCGATCT', length 12, was trimmed 3285011 times. | |
| [2014-10-05 23:55] | |
| [2014-10-05 23:55] No. of allowed errors: | |
| [2014-10-05 23:55] 0-9 bp: 0; 10-12 bp: 1 | |
| [2014-10-05 23:55] | |
| [2014-10-05 23:55] Overview of removed sequences | |
| [2014-10-05 23:55] length count expect max.err error counts | |
| [2014-10-05 23:55] 3 2365887 1050121.2 0 2365887 | |
| [2014-10-05 23:55] 4 582861 262530.3 0 582861 | |
| [2014-10-05 23:55] 5 179297 65632.6 0 179297 | |
| [2014-10-05 23:55] 6 64988 16408.1 0 64988 | |
| [2014-10-05 23:55] 7 23138 4102.0 0 23138 | |
| [2014-10-05 23:55] 8 1230 1025.5 0 1230 | |
| [2014-10-05 23:55] 9 2171 256.4 0 272 1899 | |
| [2014-10-05 23:55] 10 15447 64.1 1 398 15049 | |
| [2014-10-05 23:55] 11 3078 16.0 1 1031 2047 | |
| [2014-10-05 23:55] 12 812 4.0 1 292 520 | |
| [2014-10-05 23:55] 13 526 4.0 1 110 416 | |
| [2014-10-05 23:55] 14 1235 4.0 1 113 1122 | |
| [2014-10-05 23:55] 15 575 4.0 1 64 511 | |
| [2014-10-05 23:55] 16 2858 4.0 1 110 2748 | |
| [2014-10-05 23:55] 17 757 4.0 1 317 440 | |
| [2014-10-05 23:55] 18 435 4.0 1 96 339 | |
| [2014-10-05 23:55] 19 441 4.0 1 89 352 | |
| [2014-10-05 23:55] 20 520 4.0 1 103 417 | |
| [2014-10-05 23:55] 21 493 4.0 1 60 433 | |
| [2014-10-05 23:55] 22 495 4.0 1 59 436 | |
| [2014-10-05 23:55] 23 550 4.0 1 150 400 | |
| [2014-10-05 23:55] 24 534 4.0 1 102 432 | |
| [2014-10-05 23:55] 25 495 4.0 1 55 440 | |
| [2014-10-05 23:55] 26 376 4.0 1 39 337 | |
| [2014-10-05 23:55] 27 448 4.0 1 60 388 | |
| [2014-10-05 23:55] 28 366 4.0 1 47 319 | |
| [2014-10-05 23:55] 29 421 4.0 1 30 391 | |
| [2014-10-05 23:55] 30 494 4.0 1 59 435 | |
| [2014-10-05 23:55] 31 451 4.0 1 56 395 | |
| [2014-10-05 23:55] 32 549 4.0 1 53 496 | |
| [2014-10-05 23:55] 33 544 4.0 1 48 496 | |
| [2014-10-05 23:55] 34 490 4.0 1 55 435 | |
| [2014-10-05 23:55] 35 468 4.0 1 53 415 | |
| [2014-10-05 23:55] 36 440 4.0 1 87 353 | |
| [2014-10-05 23:55] 37 487 4.0 1 62 425 | |
| [2014-10-05 23:55] 38 517 4.0 1 229 288 | |
| [2014-10-05 23:55] 39 402 4.0 1 77 325 | |
| [2014-10-05 23:55] 40 422 4.0 1 86 336 | |
| [2014-10-05 23:55] 41 292 4.0 1 73 219 | |
| [2014-10-05 23:55] 42 361 4.0 1 59 302 | |
| [2014-10-05 23:55] 43 380 4.0 1 76 304 | |
| [2014-10-05 23:55] 44 342 4.0 1 31 311 | |
| [2014-10-05 23:55] 45 452 4.0 1 56 396 | |
| [2014-10-05 23:55] 46 369 4.0 1 34 335 | |
| [2014-10-05 23:55] 47 457 4.0 1 41 416 | |
| [2014-10-05 23:55] 48 365 4.0 1 42 323 | |
| [2014-10-05 23:55] 49 393 4.0 1 59 334 | |
| [2014-10-05 23:55] 50 345 4.0 1 57 288 | |
| [2014-10-05 23:55] 51 405 4.0 1 66 339 | |
| [2014-10-05 23:55] 52 501 4.0 1 65 436 | |
| [2014-10-05 23:55] 53 373 4.0 1 71 302 | |
| [2014-10-05 23:55] 54 385 4.0 1 50 335 | |
| [2014-10-05 23:55] 55 443 4.0 1 53 390 | |
| [2014-10-05 23:55] 56 427 4.0 1 75 352 | |
| [2014-10-05 23:55] 57 355 4.0 1 49 306 | |
| [2014-10-05 23:55] 58 427 4.0 1 48 379 | |
| [2014-10-05 23:55] 59 333 4.0 1 59 274 | |
| [2014-10-05 23:55] 60 372 4.0 1 66 306 | |
| [2014-10-05 23:55] 61 408 4.0 1 61 347 | |
| [2014-10-05 23:55] 62 405 4.0 1 62 343 | |
| [2014-10-05 23:55] 63 478 4.0 1 139 339 | |
| [2014-10-05 23:55] 64 415 4.0 1 70 345 | |
| [2014-10-05 23:55] 65 355 4.0 1 56 299 | |
| [2014-10-05 23:55] 66 311 4.0 1 34 277 | |
| [2014-10-05 23:55] 67 363 4.0 1 77 286 | |
| [2014-10-05 23:55] 68 383 4.0 1 51 332 | |
| [2014-10-05 23:55] 69 458 4.0 1 82 376 | |
| [2014-10-05 23:55] 70 381 4.0 1 77 304 | |
| [2014-10-05 23:55] 71 454 4.0 1 133 321 | |
| [2014-10-05 23:55] 72 422 4.0 1 86 336 | |
| [2014-10-05 23:55] 73 392 4.0 1 88 304 | |
| [2014-10-05 23:55] 74 542 4.0 1 141 401 | |
| [2014-10-05 23:55] 75 1128 4.0 1 754 374 | |
| [2014-10-05 23:55] 76 470 4.0 1 112 358 | |
| [2014-10-05 23:55] 77 414 4.0 1 66 348 | |
| [2014-10-05 23:55] 78 407 4.0 1 112 295 | |
| [2014-10-05 23:55] 79 469 4.0 1 139 330 | |
| [2014-10-05 23:55] 80 510 4.0 1 195 315 | |
| [2014-10-05 23:55] 81 683 4.0 1 314 369 | |
| [2014-10-05 23:55] 82 492 4.0 1 206 286 | |
| [2014-10-05 23:55] 83 856 4.0 1 352 504 | |
| [2014-10-05 23:55] 84 521 4.0 1 201 320 | |
| [2014-10-05 23:55] 85 460 4.0 1 146 314 | |
| [2014-10-05 23:55] 86 335 4.0 1 44 291 | |
| [2014-10-05 23:55] 87 476 4.0 1 50 426 | |
| [2014-10-05 23:55] 88 304 4.0 1 44 260 | |
| [2014-10-05 23:55] 89 411 4.0 1 52 359 | |
| [2014-10-05 23:55] 90 478 4.0 1 66 412 | |
| [2014-10-05 23:55] 91 435 4.0 1 80 355 | |
| [2014-10-05 23:55] 92 516 4.0 1 56 460 | |
| [2014-10-05 23:55] 93 532 4.0 1 128 404 | |
| [2014-10-05 23:55] 94 828 4.0 1 296 532 | |
| [2014-10-05 23:55] 95 437 4.0 1 130 307 | |
| [2014-10-05 23:55] 96 820 4.0 1 190 630 | |
| [2014-10-05 23:55] 97 445 4.0 1 162 283 | |
| [2014-10-05 23:55] 98 1940 4.0 1 1424 516 | |
| [2014-10-05 23:55] 99 524 4.0 1 70 454 | |
| [2014-10-05 23:55] 100 574 4.0 1 402 172 | |
| [2014-10-05 23:55] 101 304 4.0 1 66 238 | |
| [2014-10-05 23:55] | |
| [2014-10-06 00:38] cutadapt version 1.4.2 | |
| [2014-10-06 00:38] Command line parameters: --times=2 --quality-base=33 --quality-cutoff=5 --format=fastq --adapter=AAAAAAAAAAAAA --adapter=TTTTTTTTTTTTT --adapter=AGATCGGAAGAG --adapter=CTCTTCCGATCT --minimum-length=25 -o /vagrant_data/seqc-test/seqc/work/trimmed/SRR950083_1.trimmed.tmp.fastq.gz -p /vagrant_data/seqc-test/seqc/work/trimmed/SRR950083_2.trimmed.tmp.fastq.gz /vagrant_data/seqc-test/input/SRR950083_1.fastq.gz /vagrant_data/seqc-test/input/SRR950083_2.fastq.gz | |
| [2014-10-06 00:38] Maximum error rate: 10.00% | |
| [2014-10-06 00:38] No. of adapters: 4 | |
| [2014-10-06 00:38] Processed reads: 113161956 | |
| [2014-10-06 00:38] Processed bases: 11429357556 bp (11429.4 Mbp) | |
| [2014-10-06 00:38] Trimmed reads: 16774127 (14.8%) | |
| [2014-10-06 00:38] Quality-trimmed: 1275553515 bp (1275.6 Mbp) (11.16% of total) | |
| [2014-10-06 00:38] Trimmed bases: 505526025 bp (505.5 Mbp) (4.42% of total) | |
| [2014-10-06 00:38] Too short reads: 9598247 (8.5% of processed reads) | |
| [2014-10-06 00:38] Too long reads: 0 (0.0% of processed reads) | |
| [2014-10-06 00:38] Total time: 6275.96 s | |
| [2014-10-06 00:38] Time per read: 0.055 ms | |
| [2014-10-06 00:38] | |
| [2014-10-06 00:38] === Adapter 1 === | |
| [2014-10-06 00:38] | |
| [2014-10-06 00:38] Adapter 'AAAAAAAAAAAAA', length 13, was trimmed 7950859 times. | |
| [2014-10-06 00:38] | |
| [2014-10-06 00:38] No. of allowed errors: | |
| [2014-10-06 00:38] 0-9 bp: 0; 10-13 bp: 1 | |
| [2014-10-06 00:38] | |
| [2014-10-06 00:38] Overview of removed sequences | |
| [2014-10-06 00:38] length count expect max.err error counts | |
| [2014-10-06 00:38] 3 3973066 1768155.6 0 3973066 | |
| [2014-10-06 00:38] 4 1440830 442038.9 0 1440830 | |
| [2014-10-06 00:38] 5 590064 110509.7 0 590064 | |
| [2014-10-06 00:38] 6 211775 27627.4 0 211775 | |
| [2014-10-06 00:38] 7 105644 6906.9 0 105644 | |
| [2014-10-06 00:38] 8 56075 1726.7 0 56075 | |
| [2014-10-06 00:38] 9 46377 431.7 0 46377 | |
| [2014-10-06 00:38] 10 116759 107.9 1 37874 78885 | |
| [2014-10-06 00:38] 11 85766 27.0 1 35179 50587 | |
| [2014-10-06 00:38] 12 76232 6.7 1 43416 32816 | |
| [2014-10-06 00:38] 13 64220 1.7 1 42815 21405 | |
| [2014-10-06 00:38] 14 59919 1.7 1 42611 17308 | |
| [2014-10-06 00:38] 15 55094 1.7 1 40564 14530 | |
| [2014-10-06 00:38] 16 50025 1.7 1 36435 13590 | |
| [2014-10-06 00:38] 17 43239 1.7 1 31622 11617 | |
| [2014-10-06 00:38] 18 40978 1.7 1 27872 13106 | |
| [2014-10-06 00:38] 19 34612 1.7 1 24431 10181 | |
| [2014-10-06 00:38] 20 31869 1.7 1 22099 9770 | |
| [2014-10-06 00:38] 21 29868 1.7 1 20352 9516 | |
| [2014-10-06 00:38] 22 27699 1.7 1 18234 9465 | |
| [2014-10-06 00:38] 23 25604 1.7 1 16364 9240 | |
| [2014-10-06 00:38] 24 23475 1.7 1 14600 8875 | |
| [2014-10-06 00:38] 25 22141 1.7 1 13406 8735 | |
| [2014-10-06 00:38] 26 21334 1.7 1 12215 9119 | |
| [2014-10-06 00:38] 27 19081 1.7 1 10730 8351 | |
| [2014-10-06 00:38] 28 17877 1.7 1 9533 8344 | |
| [2014-10-06 00:38] 29 17094 1.7 1 8821 8273 | |
| [2014-10-06 00:38] 30 16955 1.7 1 8297 8658 | |
| [2014-10-06 00:38] 31 16119 1.7 1 7600 8519 | |
| [2014-10-06 00:38] 32 14962 1.7 1 7031 7931 | |
| [2014-10-06 00:38] 33 15081 1.7 1 7067 8014 | |
| [2014-10-06 00:38] 34 14310 1.7 1 6364 7946 | |
| [2014-10-06 00:38] 35 13564 1.7 1 6443 7121 | |
| [2014-10-06 00:38] 36 12954 1.7 1 5450 7504 | |
| [2014-10-06 00:38] 37 12965 1.7 1 5572 7393 | |
| [2014-10-06 00:38] 38 13216 1.7 1 5286 7930 | |
| [2014-10-06 00:38] 39 12228 1.7 1 4808 7420 | |
| [2014-10-06 00:38] 40 11761 1.7 1 5036 6725 | |
| [2014-10-06 00:38] 41 11293 1.7 1 4476 6817 | |
| [2014-10-06 00:38] 42 10751 1.7 1 4264 6487 | |
| [2014-10-06 00:38] 43 11404 1.7 1 4667 6737 | |
| [2014-10-06 00:38] 44 11595 1.7 1 4720 6875 | |
| [2014-10-06 00:38] 45 10898 1.7 1 4258 6640 | |
| [2014-10-06 00:38] 46 10312 1.7 1 3655 6657 | |
| [2014-10-06 00:38] 47 10085 1.7 1 3513 6572 | |
| [2014-10-06 00:38] 48 10279 1.7 1 3396 6883 | |
| [2014-10-06 00:38] 49 9588 1.7 1 3003 6585 | |
| [2014-10-06 00:38] 50 9125 1.7 1 2673 6452 | |
| [2014-10-06 00:38] 51 9368 1.7 1 2789 6579 | |
| [2014-10-06 00:38] 52 8683 1.7 1 2503 6180 | |
| [2014-10-06 00:38] 53 8910 1.7 1 2633 6277 | |
| [2014-10-06 00:38] 54 8920 1.7 1 2469 6451 | |
| [2014-10-06 00:38] 55 9228 1.7 1 2649 6579 | |
| [2014-10-06 00:38] 56 8815 1.7 1 2466 6349 | |
| [2014-10-06 00:38] 57 8551 1.7 1 2196 6355 | |
| [2014-10-06 00:38] 58 8661 1.7 1 2260 6401 | |
| [2014-10-06 00:38] 59 8469 1.7 1 2264 6205 | |
| [2014-10-06 00:38] 60 8754 1.7 1 2377 6377 | |
| [2014-10-06 00:38] 61 8458 1.7 1 2316 6142 | |
| [2014-10-06 00:38] 62 8951 1.7 1 2416 6535 | |
| [2014-10-06 00:38] 63 8513 1.7 1 2298 6215 | |
| [2014-10-06 00:38] 64 8435 1.7 1 2233 6202 | |
| [2014-10-06 00:38] 65 7955 1.7 1 2044 5911 | |
| [2014-10-06 00:38] 66 8494 1.7 1 2187 6307 | |
| [2014-10-06 00:38] 67 8276 1.7 1 2229 6047 | |
| [2014-10-06 00:38] 68 8404 1.7 1 2204 6200 | |
| [2014-10-06 00:38] 69 8505 1.7 1 1931 6574 | |
| [2014-10-06 00:38] 70 8313 1.7 1 1835 6478 | |
| [2014-10-06 00:38] 71 9128 1.7 1 1885 7243 | |
| [2014-10-06 00:38] 72 9051 1.7 1 1943 7108 | |
| [2014-10-06 00:38] 73 8647 1.7 1 1804 6843 | |
| [2014-10-06 00:38] 74 8475 1.7 1 1741 6734 | |
| [2014-10-06 00:38] 75 7732 1.7 1 1608 6124 | |
| [2014-10-06 00:38] 76 8445 1.7 1 1736 6709 | |
| [2014-10-06 00:38] 77 7998 1.7 1 1444 6554 | |
| [2014-10-06 00:38] 78 7810 1.7 1 1494 6316 | |
| [2014-10-06 00:38] 79 7652 1.7 1 1535 6117 | |
| [2014-10-06 00:38] 80 7931 1.7 1 1470 6461 | |
| [2014-10-06 00:38] 81 7682 1.7 1 1417 6265 | |
| [2014-10-06 00:38] 82 7910 1.7 1 1539 6371 | |
| [2014-10-06 00:38] 83 7572 1.7 1 1443 6129 | |
| [2014-10-06 00:38] 84 7203 1.7 1 1589 5614 | |
| [2014-10-06 00:38] 85 7617 1.7 1 1470 6147 | |
| [2014-10-06 00:38] 86 7544 1.7 1 1505 6039 | |
| [2014-10-06 00:38] 87 7707 1.7 1 1498 6209 | |
| [2014-10-06 00:38] 88 7061 1.7 1 1345 5716 | |
| [2014-10-06 00:38] 89 7305 1.7 1 1190 6115 | |
| [2014-10-06 00:38] 90 5931 1.7 1 1119 4812 | |
| [2014-10-06 00:38] 91 5395 1.7 1 1027 4368 | |
| [2014-10-06 00:38] 92 8647 1.7 1 1574 7073 | |
| [2014-10-06 00:38] 93 9143 1.7 1 1516 7627 | |
| [2014-10-06 00:38] 94 8973 1.7 1 1213 7760 | |
| [2014-10-06 00:38] 95 4707 1.7 1 733 3974 | |
| [2014-10-06 00:38] 96 3788 1.7 1 550 3238 | |
| [2014-10-06 00:38] 97 4436 1.7 1 589 3847 | |
| [2014-10-06 00:38] 98 4270 1.7 1 640 3630 | |
| [2014-10-06 00:38] 99 4194 1.7 1 466 3728 | |
| [2014-10-06 00:38] 100 7538 1.7 1 728 6810 | |
| [2014-10-06 00:38] 101 14542 1.7 1 1626 12916 | |
| [2014-10-06 00:38] | |
| [2014-10-06 00:38] === Adapter 2 === | |
| [2014-10-06 00:38] | |
| [2014-10-06 00:38] Adapter 'TTTTTTTTTTTTT', length 13, was trimmed 7960146 times. | |
| [2014-10-06 00:38] | |
| [2014-10-06 00:38] No. of allowed errors: | |
| [2014-10-06 00:38] 0-9 bp: 0; 10-13 bp: 1 | |
| [2014-10-06 00:38] | |
| [2014-10-06 00:38] Overview of removed sequences | |
| [2014-10-06 00:38] length count expect max.err error counts | |
| [2014-10-06 00:38] 3 3937589 1768155.6 0 3937589 | |
| [2014-10-06 00:38] 4 1435354 442038.9 0 1435354 | |
| [2014-10-06 00:38] 5 532832 110509.7 0 532832 | |
| [2014-10-06 00:38] 6 191118 27627.4 0 191118 | |
| [2014-10-06 00:38] 7 111463 6906.9 0 111463 | |
| [2014-10-06 00:38] 8 42749 1726.7 0 42749 | |
| [2014-10-06 00:38] 9 33396 431.7 0 33396 | |
| [2014-10-06 00:38] 10 108360 107.9 1 29795 78565 | |
| [2014-10-06 00:38] 11 76363 27.0 1 27721 48642 | |
| [2014-10-06 00:38] 12 79023 6.7 1 45266 33757 | |
| [2014-10-06 00:38] 13 71962 1.7 1 49096 22866 | |
| [2014-10-06 00:38] 14 74490 1.7 1 55793 18697 | |
| [2014-10-06 00:38] 15 74120 1.7 1 58595 15525 | |
| [2014-10-06 00:38] 16 67873 1.7 1 54850 13023 | |
| [2014-10-06 00:38] 17 62145 1.7 1 50535 11610 | |
| [2014-10-06 00:38] 18 51661 1.7 1 40780 10881 | |
| [2014-10-06 00:38] 19 43868 1.7 1 32555 11313 | |
| [2014-10-06 00:38] 20 43290 1.7 1 29352 13938 | |
| [2014-10-06 00:38] 21 37877 1.7 1 26835 11042 | |
| [2014-10-06 00:38] 22 33344 1.7 1 23131 10213 | |
| [2014-10-06 00:38] 23 30359 1.7 1 20506 9853 | |
| [2014-10-06 00:38] 24 28910 1.7 1 18407 10503 | |
| [2014-10-06 00:38] 25 25621 1.7 1 15692 9929 | |
| [2014-10-06 00:38] 26 23462 1.7 1 13381 10081 | |
| [2014-10-06 00:38] 27 20627 1.7 1 11737 8890 | |
| [2014-10-06 00:38] 28 19196 1.7 1 10070 9126 | |
| [2014-10-06 00:38] 29 17934 1.7 1 9113 8821 | |
| [2014-10-06 00:38] 30 16617 1.7 1 7741 8876 | |
| [2014-10-06 00:38] 31 15484 1.7 1 7179 8305 | |
| [2014-10-06 00:38] 32 14745 1.7 1 6532 8213 | |
| [2014-10-06 00:38] 33 13890 1.7 1 5637 8253 | |
| [2014-10-06 00:38] 34 13241 1.7 1 5114 8127 | |
| [2014-10-06 00:38] 35 11953 1.7 1 4485 7468 | |
| [2014-10-06 00:38] 36 12170 1.7 1 4091 8079 | |
| [2014-10-06 00:38] 37 11472 1.7 1 3942 7530 | |
| [2014-10-06 00:38] 38 12378 1.7 1 3905 8473 | |
| [2014-10-06 00:38] 39 12446 1.7 1 3959 8487 | |
| [2014-10-06 00:38] 40 12493 1.7 1 4065 8428 | |
| [2014-10-06 00:38] 41 11797 1.7 1 3848 7949 | |
| [2014-10-06 00:38] 42 12054 1.7 1 3738 8316 | |
| [2014-10-06 00:38] 43 12090 1.7 1 3647 8443 | |
| [2014-10-06 00:38] 44 11636 1.7 1 3516 8120 | |
| [2014-10-06 00:38] 45 10976 1.7 1 3307 7669 | |
| [2014-10-06 00:38] 46 10903 1.7 1 3503 7400 | |
| [2014-10-06 00:38] 47 10819 1.7 1 3237 7582 | |
| [2014-10-06 00:38] 48 10700 1.7 1 3123 7577 | |
| [2014-10-06 00:38] 49 10166 1.7 1 2877 7289 | |
| [2014-10-06 00:38] 50 10565 1.7 1 2869 7696 | |
| [2014-10-06 00:38] 51 9492 1.7 1 2652 6840 | |
| [2014-10-06 00:38] 52 9191 1.7 1 2382 6809 | |
| [2014-10-06 00:38] 53 9262 1.7 1 2488 6774 | |
| [2014-10-06 00:38] 54 9662 1.7 1 2349 7313 | |
| [2014-10-06 00:38] 55 9268 1.7 1 2346 6922 | |
| [2014-10-06 00:38] 56 9759 1.7 1 2290 7469 | |
| [2014-10-06 00:38] 57 9486 1.7 1 2072 7414 | |
| [2014-10-06 00:38] 58 9140 1.7 1 1936 7204 | |
| [2014-10-06 00:38] 59 8934 1.7 1 1894 7040 | |
| [2014-10-06 00:38] 60 8870 1.7 1 1936 6934 | |
| [2014-10-06 00:38] 61 9181 1.7 1 1900 7281 | |
| [2014-10-06 00:38] 62 8362 1.7 1 1870 6492 | |
| [2014-10-06 00:38] 63 8446 1.7 1 1869 6577 | |
| [2014-10-06 00:38] 64 9083 1.7 1 1783 7300 | |
| [2014-10-06 00:38] 65 8687 1.7 1 1665 7022 | |
| [2014-10-06 00:38] 66 8947 1.7 1 1721 7226 | |
| [2014-10-06 00:38] 67 8288 1.7 1 1532 6756 | |
| [2014-10-06 00:38] 68 10814 1.7 1 1507 9307 | |
| [2014-10-06 00:38] 69 10151 1.7 1 1648 8503 | |
| [2014-10-06 00:38] 70 8662 1.7 1 1570 7092 | |
| [2014-10-06 00:38] 71 8856 1.7 1 1641 7215 | |
| [2014-10-06 00:38] 72 8256 1.7 1 1615 6641 | |
| [2014-10-06 00:38] 73 8368 1.7 1 1439 6929 | |
| [2014-10-06 00:38] 74 8225 1.7 1 1461 6764 | |
| [2014-10-06 00:38] 75 7537 1.7 1 1281 6256 | |
| [2014-10-06 00:38] 76 8071 1.7 1 1358 6713 | |
| [2014-10-06 00:38] 77 8098 1.7 1 1440 6658 | |
| [2014-10-06 00:38] 78 10375 1.7 1 1451 8924 | |
| [2014-10-06 00:38] 79 7791 1.7 1 1619 6172 | |
| [2014-10-06 00:38] 80 7979 1.7 1 1392 6587 | |
| [2014-10-06 00:38] 81 7792 1.7 1 1269 6523 | |
| [2014-10-06 00:38] 82 8091 1.7 1 1136 6955 | |
| [2014-10-06 00:38] 83 7720 1.7 1 1234 6486 | |
| [2014-10-06 00:38] 84 9303 1.7 1 1200 8103 | |
| [2014-10-06 00:38] 85 7192 1.7 1 1155 6037 | |
| [2014-10-06 00:38] 86 6948 1.7 1 1084 5864 | |
| [2014-10-06 00:38] 87 7137 1.7 1 1023 6114 | |
| [2014-10-06 00:38] 88 7104 1.7 1 1078 6026 | |
| [2014-10-06 00:38] 89 7601 1.7 1 1010 6591 | |
| [2014-10-06 00:38] 90 9314 1.7 1 1172 8142 | |
| [2014-10-06 00:38] 91 8273 1.7 1 1090 7183 | |
| [2014-10-06 00:38] 92 7939 1.7 1 1034 6905 | |
| [2014-10-06 00:38] 93 6759 1.7 1 947 5812 | |
| [2014-10-06 00:38] 94 4419 1.7 1 741 3678 | |
| [2014-10-06 00:38] 95 6116 1.7 1 796 5320 | |
| [2014-10-06 00:38] 96 5966 1.7 1 758 5208 | |
| [2014-10-06 00:38] 97 5735 1.7 1 587 5148 | |
| [2014-10-06 00:38] 98 3739 1.7 1 508 3231 | |
| [2014-10-06 00:38] 99 3348 1.7 1 506 2842 | |
| [2014-10-06 00:38] 100 12762 1.7 1 928 11834 | |
| [2014-10-06 00:38] 101 16066 1.7 1 2928 13138 | |
| [2014-10-06 00:38] | |
| [2014-10-06 00:38] === Adapter 3 === | |
| [2014-10-06 00:38] | |
| [2014-10-06 00:38] Adapter 'AGATCGGAAGAG', length 12, was trimmed 11665404 times. | |
| [2014-10-06 00:38] | |
| [2014-10-06 00:38] No. of allowed errors: | |
| [2014-10-06 00:38] 0-9 bp: 0; 10-12 bp: 1 | |
| [2014-10-06 00:38] | |
| [2014-10-06 00:38] Overview of removed sequences | |
| [2014-10-06 00:38] length count expect max.err error counts | |
| [2014-10-06 00:38] 3 4230700 1768155.6 0 4230700 | |
| [2014-10-06 00:38] 4 1028744 442038.9 0 1028744 | |
| [2014-10-06 00:38] 5 349106 110509.7 0 349106 | |
| [2014-10-06 00:38] 6 267137 27627.4 0 267137 | |
| [2014-10-06 00:38] 7 188403 6906.9 0 188403 | |
| [2014-10-06 00:38] 8 216895 1726.7 0 216895 | |
| [2014-10-06 00:38] 9 166157 431.7 0 160004 6153 | |
| [2014-10-06 00:38] 10 137765 107.9 1 128011 9754 | |
| [2014-10-06 00:38] 11 107791 27.0 1 101021 6770 | |
| [2014-10-06 00:38] 12 104251 6.7 1 99714 4537 | |
| [2014-10-06 00:38] 13 72918 6.7 1 68922 3996 | |
| [2014-10-06 00:38] 14 74108 6.7 1 70934 3174 | |
| [2014-10-06 00:38] 15 65589 6.7 1 61898 3691 | |
| [2014-10-06 00:38] 16 59394 6.7 1 55961 3433 | |
| [2014-10-06 00:38] 17 61859 6.7 1 58194 3665 | |
| [2014-10-06 00:38] 18 55511 6.7 1 52805 2706 | |
| [2014-10-06 00:38] 19 37973 6.7 1 35721 2252 | |
| [2014-10-06 00:38] 20 38188 6.7 1 35545 2643 | |
| [2014-10-06 00:38] 21 32796 6.7 1 30162 2634 | |
| [2014-10-06 00:38] 22 31184 6.7 1 24564 6620 | |
| [2014-10-06 00:38] 23 28703 6.7 1 24965 3738 | |
| [2014-10-06 00:38] 24 23012 6.7 1 20367 2645 | |
| [2014-10-06 00:38] 25 21690 6.7 1 19290 2400 | |
| [2014-10-06 00:38] 26 18599 6.7 1 15757 2842 | |
| [2014-10-06 00:38] 27 25955 6.7 1 20704 5251 | |
| [2014-10-06 00:38] 28 22867 6.7 1 19095 3772 | |
| [2014-10-06 00:38] 29 21823 6.7 1 17745 4078 | |
| [2014-10-06 00:38] 30 20889 6.7 1 17905 2984 | |
| [2014-10-06 00:38] 31 13051 6.7 1 10272 2779 | |
| [2014-10-06 00:38] 32 13581 6.7 1 10066 3515 | |
| [2014-10-06 00:38] 33 15524 6.7 1 8938 6586 | |
| [2014-10-06 00:38] 34 16404 6.7 1 11354 5050 | |
| [2014-10-06 00:38] 35 16069 6.7 1 10681 5388 | |
| [2014-10-06 00:38] 36 15652 6.7 1 9682 5970 | |
| [2014-10-06 00:38] 37 13809 6.7 1 7522 6287 | |
| [2014-10-06 00:38] 38 16772 6.7 1 8559 8213 | |
| [2014-10-06 00:38] 39 26784 6.7 1 11354 15430 | |
| [2014-10-06 00:38] 40 23672 6.7 1 11182 12490 | |
| [2014-10-06 00:38] 41 18504 6.7 1 11527 6977 | |
| [2014-10-06 00:38] 42 13648 6.7 1 7582 6066 | |
| [2014-10-06 00:38] 43 12142 6.7 1 7060 5082 | |
| [2014-10-06 00:38] 44 13966 6.7 1 5472 8494 | |
| [2014-10-06 00:38] 45 13554 6.7 1 6596 6958 | |
| [2014-10-06 00:38] 46 10841 6.7 1 6364 4477 | |
| [2014-10-06 00:38] 47 9062 6.7 1 4273 4789 | |
| [2014-10-06 00:38] 48 11319 6.7 1 5198 6121 | |
| [2014-10-06 00:38] 49 10069 6.7 1 5482 4587 | |
| [2014-10-06 00:38] 50 12353 6.7 1 4021 8332 | |
| [2014-10-06 00:38] 51 19286 6.7 1 5671 13615 | |
| [2014-10-06 00:38] 52 18121 6.7 1 6682 11439 | |
| [2014-10-06 00:38] 53 11195 6.7 1 6826 4369 | |
| [2014-10-06 00:38] 54 7627 6.7 1 2977 4650 | |
| [2014-10-06 00:38] 55 9638 6.7 1 2727 6911 | |
| [2014-10-06 00:38] 56 13707 6.7 1 4512 9195 | |
| [2014-10-06 00:38] 57 15165 6.7 1 4632 10533 | |
| [2014-10-06 00:38] 58 19662 6.7 1 5375 14287 | |
| [2014-10-06 00:38] 59 17219 6.7 1 6634 10585 | |
| [2014-10-06 00:38] 60 19616 6.7 1 4736 14880 | |
| [2014-10-06 00:38] 61 26380 6.7 1 6304 20076 | |
| [2014-10-06 00:38] 62 62562 6.7 1 9366 53196 | |
| [2014-10-06 00:38] 63 105101 6.7 1 19903 85198 | |
| [2014-10-06 00:38] 64 63224 6.7 1 28480 34744 | |
| [2014-10-06 00:38] 65 55505 6.7 1 13174 42331 | |
| [2014-10-06 00:38] 66 86176 6.7 1 16285 69891 | |
| [2014-10-06 00:38] 67 147876 6.7 1 26536 121340 | |
| [2014-10-06 00:38] 68 293463 6.7 1 49074 244389 | |
| [2014-10-06 00:38] 69 622896 6.7 1 87590 535306 | |
| [2014-10-06 00:38] 70 571660 6.7 1 163017 408643 | |
| [2014-10-06 00:38] 71 607403 6.7 1 125399 482004 | |
| [2014-10-06 00:38] 72 581954 6.7 1 146883 435071 | |
| [2014-10-06 00:38] 73 337131 6.7 1 129729 207402 | |
| [2014-10-06 00:38] 74 61941 6.7 1 55676 6265 | |
| [2014-10-06 00:38] 75 4684 6.7 1 3632 1052 | |
| [2014-10-06 00:38] 76 2085 6.7 1 920 1165 | |
| [2014-10-06 00:38] 77 1749 6.7 1 362 1387 | |
| [2014-10-06 00:38] 78 1681 6.7 1 317 1364 | |
| [2014-10-06 00:38] 79 1633 6.7 1 314 1319 | |
| [2014-10-06 00:38] 80 1654 6.7 1 302 1352 | |
| [2014-10-06 00:38] 81 1802 6.7 1 317 1485 | |
| [2014-10-06 00:38] 82 1901 6.7 1 334 1567 | |
| [2014-10-06 00:38] 83 1938 6.7 1 290 1648 | |
| [2014-10-06 00:38] 84 2021 6.7 1 338 1683 | |
| [2014-10-06 00:38] 85 1984 6.7 1 335 1649 | |
| [2014-10-06 00:38] 86 2199 6.7 1 379 1820 | |
| [2014-10-06 00:38] 87 2307 6.7 1 360 1947 | |
| [2014-10-06 00:38] 88 2414 6.7 1 408 2006 | |
| [2014-10-06 00:38] 89 2581 6.7 1 496 2085 | |
| [2014-10-06 00:38] 90 2624 6.7 1 464 2160 | |
| [2014-10-06 00:38] 91 2853 6.7 1 501 2352 | |
| [2014-10-06 00:38] 92 3101 6.7 1 534 2567 | |
| [2014-10-06 00:38] 93 2923 6.7 1 592 2331 | |
| [2014-10-06 00:38] 94 3100 6.7 1 540 2560 | |
| [2014-10-06 00:38] 95 3051 6.7 1 561 2490 | |
| [2014-10-06 00:38] 96 3238 6.7 1 548 2690 | |
| [2014-10-06 00:38] 97 2918 6.7 1 520 2398 | |
| [2014-10-06 00:38] 98 3696 6.7 1 562 3134 | |
| [2014-10-06 00:38] 99 2290 6.7 1 442 1848 | |
| [2014-10-06 00:38] 100 1448 6.7 1 294 1154 | |
| [2014-10-06 00:38] 101 20238 6.7 1 4354 15884 | |
| [2014-10-06 00:38] | |
| [2014-10-06 00:38] === Adapter 4 === | |
| [2014-10-06 00:38] | |
| [2014-10-06 00:38] Adapter 'CTCTTCCGATCT', length 12, was trimmed 5971845 times. | |
| [2014-10-06 00:38] | |
| [2014-10-06 00:38] No. of allowed errors: | |
| [2014-10-06 00:38] 0-9 bp: 0; 10-12 bp: 1 | |
| [2014-10-06 00:38] | |
| [2014-10-06 00:38] Overview of removed sequences | |
| [2014-10-06 00:38] length count expect max.err error counts | |
| [2014-10-06 00:38] 3 4317944 1768155.6 0 4317944 | |
| [2014-10-06 00:38] 4 1092277 442038.9 0 1092277 | |
| [2014-10-06 00:38] 5 322972 110509.7 0 322972 | |
| [2014-10-06 00:38] 6 112864 27627.4 0 112864 | |
| [2014-10-06 00:38] 7 39038 6906.9 0 39038 | |
| [2014-10-06 00:38] 8 1964 1726.7 0 1964 | |
| [2014-10-06 00:38] 9 3474 431.7 0 306 3168 | |
| [2014-10-06 00:38] 10 21485 107.9 1 60 21425 | |
| [2014-10-06 00:38] 11 2318 27.0 1 68 2250 | |
| [2014-10-06 00:38] 12 735 6.7 1 66 669 | |
| [2014-10-06 00:38] 13 555 6.7 1 14 541 | |
| [2014-10-06 00:38] 14 557 6.7 1 14 543 | |
| [2014-10-06 00:38] 15 540 6.7 1 7 533 | |
| [2014-10-06 00:38] 16 547 6.7 1 5 542 | |
| [2014-10-06 00:38] 17 607 6.7 1 12 595 | |
| [2014-10-06 00:38] 18 508 6.7 1 17 491 | |
| [2014-10-06 00:38] 19 586 6.7 1 23 563 | |
| [2014-10-06 00:38] 20 580 6.7 1 26 554 | |
| [2014-10-06 00:38] 21 585 6.7 1 12 573 | |
| [2014-10-06 00:38] 22 707 6.7 1 11 696 | |
| [2014-10-06 00:38] 23 678 6.7 1 36 642 | |
| [2014-10-06 00:38] 24 666 6.7 1 16 650 | |
| [2014-10-06 00:38] 25 645 6.7 1 7 638 | |
| [2014-10-06 00:38] 26 520 6.7 1 18 502 | |
| [2014-10-06 00:38] 27 562 6.7 1 15 547 | |
| [2014-10-06 00:38] 28 602 6.7 1 11 591 | |
| [2014-10-06 00:38] 29 669 6.7 1 11 658 | |
| [2014-10-06 00:38] 30 677 6.7 1 8 669 | |
| [2014-10-06 00:38] 31 714 6.7 1 6 708 | |
| [2014-10-06 00:38] 32 735 6.7 1 14 721 | |
| [2014-10-06 00:38] 33 648 6.7 1 11 637 | |
| [2014-10-06 00:38] 34 674 6.7 1 18 656 | |
| [2014-10-06 00:38] 35 724 6.7 1 5 719 | |
| [2014-10-06 00:38] 36 569 6.7 1 13 556 | |
| [2014-10-06 00:38] 37 617 6.7 1 20 597 | |
| [2014-10-06 00:38] 38 612 6.7 1 36 576 | |
| [2014-10-06 00:38] 39 730 6.7 1 20 710 | |
| [2014-10-06 00:38] 40 568 6.7 1 34 534 | |
| [2014-10-06 00:38] 41 532 6.7 1 13 519 | |
| [2014-10-06 00:38] 42 581 6.7 1 15 566 | |
| [2014-10-06 00:38] 43 482 6.7 1 5 477 | |
| [2014-10-06 00:38] 44 613 6.7 1 11 602 | |
| [2014-10-06 00:38] 45 628 6.7 1 9 619 | |
| [2014-10-06 00:38] 46 632 6.7 1 6 626 | |
| [2014-10-06 00:38] 47 779 6.7 1 11 768 | |
| [2014-10-06 00:38] 48 602 6.7 1 14 588 | |
| [2014-10-06 00:38] 49 622 6.7 1 14 608 | |
| [2014-10-06 00:38] 50 511 6.7 1 11 500 | |
| [2014-10-06 00:38] 51 529 6.7 1 12 517 | |
| [2014-10-06 00:38] 52 771 6.7 1 23 748 | |
| [2014-10-06 00:38] 53 813 6.7 1 18 795 | |
| [2014-10-06 00:38] 54 602 6.7 1 22 580 | |
| [2014-10-06 00:38] 55 665 6.7 1 14 651 | |
| [2014-10-06 00:38] 56 545 6.7 1 11 534 | |
| [2014-10-06 00:38] 57 506 6.7 1 12 494 | |
| [2014-10-06 00:38] 58 619 6.7 1 17 602 | |
| [2014-10-06 00:38] 59 565 6.7 1 14 551 | |
| [2014-10-06 00:38] 60 545 6.7 1 12 533 | |
| [2014-10-06 00:38] 61 605 6.7 1 25 580 | |
| [2014-10-06 00:38] 62 556 6.7 1 14 542 | |
| [2014-10-06 00:38] 63 542 6.7 1 24 518 | |
| [2014-10-06 00:38] 64 538 6.7 1 25 513 | |
| [2014-10-06 00:38] 65 568 6.7 1 14 554 | |
| [2014-10-06 00:38] 66 542 6.7 1 20 522 | |
| [2014-10-06 00:38] 67 652 6.7 1 17 635 | |
| [2014-10-06 00:38] 68 524 6.7 1 14 510 | |
| [2014-10-06 00:38] 69 539 6.7 1 18 521 | |
| [2014-10-06 00:38] 70 502 6.7 1 14 488 | |
| [2014-10-06 00:38] 71 564 6.7 1 16 548 | |
| [2014-10-06 00:38] 72 549 6.7 1 8 541 | |
| [2014-10-06 00:38] 73 470 6.7 1 13 457 | |
| [2014-10-06 00:38] 74 573 6.7 1 18 555 | |
| [2014-10-06 00:38] 75 682 6.7 1 23 659 | |
| [2014-10-06 00:38] 76 647 6.7 1 10 637 | |
| [2014-10-06 00:38] 77 637 6.7 1 28 609 | |
| [2014-10-06 00:38] 78 464 6.7 1 23 441 | |
| [2014-10-06 00:38] 79 601 6.7 1 47 554 | |
| [2014-10-06 00:38] 80 518 6.7 1 44 474 | |
| [2014-10-06 00:38] 81 704 6.7 1 68 636 | |
| [2014-10-06 00:38] 82 692 6.7 1 44 648 | |
| [2014-10-06 00:38] 83 953 6.7 1 63 890 | |
| [2014-10-06 00:38] 84 509 6.7 1 44 465 | |
| [2014-10-06 00:38] 85 611 6.7 1 48 563 | |
| [2014-10-06 00:38] 86 544 6.7 1 19 525 | |
| [2014-10-06 00:38] 87 565 6.7 1 32 533 | |
| [2014-10-06 00:38] 88 563 6.7 1 36 527 | |
| [2014-10-06 00:38] 89 654 6.7 1 50 604 | |
| [2014-10-06 00:38] 90 633 6.7 1 44 589 | |
| [2014-10-06 00:38] 91 677 6.7 1 72 605 | |
| [2014-10-06 00:38] 92 566 6.7 1 74 492 | |
| [2014-10-06 00:38] 93 749 6.7 1 150 599 | |
| [2014-10-06 00:38] 94 1049 6.7 1 262 787 | |
| [2014-10-06 00:38] 95 656 6.7 1 128 528 | |
| [2014-10-06 00:38] 96 1223 6.7 1 194 1029 | |
| [2014-10-06 00:38] 97 592 6.7 1 166 426 | |
| [2014-10-06 00:38] 98 2351 6.7 1 1502 849 | |
| [2014-10-06 00:38] 99 732 6.7 1 76 656 | |
| [2014-10-06 00:38] 100 458 6.7 1 184 274 | |
| [2014-10-06 00:38] 101 496 6.7 1 98 398 | |
| [2014-10-06 00:38] | |
| [2014-10-06 00:55] cutadapt version 1.4.2 | |
| [2014-10-06 00:55] Command line parameters: --times=2 --quality-base=33 --quality-cutoff=5 --format=fastq --adapter=AAAAAAAAAAAAA --adapter=TTTTTTTTTTTTT --adapter=AGATCGGAAGAG --adapter=CTCTTCCGATCT --minimum-length=25 -o /vagrant_data/seqc-test/seqc/work/trimmed/SRR950082_2.trimmed.fastq.gz -p /vagrant_data/seqc-test/seqc/work/trimmed/SRR950082_1.trimmed.fastq.gz /vagrant_data/seqc-test/seqc/work/trimmed/SRR950082_2.trimmed.tmp.fastq.gz /vagrant_data/seqc-test/seqc/work/trimmed/SRR950082_1.trimmed.tmp.fastq.gz | |
| [2014-10-06 00:55] Maximum error rate: 10.00% | |
| [2014-10-06 00:55] No. of adapters: 4 | |
| [2014-10-06 00:55] Processed reads: 57775112 | |
| [2014-10-06 00:55] Processed bases: 5835286312 bp (5835.3 Mbp) | |
| [2014-10-06 00:55] Trimmed reads: 8190476 (14.2%) | |
| [2014-10-06 00:55] Quality-trimmed: 228149625 bp (228.1 Mbp) (3.91% of total) | |
| [2014-10-06 00:55] Trimmed bases: 153110971 bp (153.1 Mbp) (2.62% of total) | |
| [2014-10-06 00:55] Too short reads: 1171684 (2.0% of processed reads) | |
| [2014-10-06 00:55] Too long reads: 0 (0.0% of processed reads) | |
| [2014-10-06 00:55] Total time: 3368.05 s | |
| [2014-10-06 00:55] Time per read: 0.058 ms | |
| [2014-10-06 00:55] | |
| [2014-10-06 00:55] === Adapter 1 === | |
| [2014-10-06 00:55] | |
| [2014-10-06 00:55] Adapter 'AAAAAAAAAAAAA', length 13, was trimmed 3573010 times. | |
| [2014-10-06 00:55] | |
| [2014-10-06 00:55] No. of allowed errors: | |
| [2014-10-06 00:55] 0-9 bp: 0; 10-13 bp: 1 | |
| [2014-10-06 00:55] | |
| [2014-10-06 00:55] Overview of removed sequences | |
| [2014-10-06 00:55] length count expect max.err error counts | |
| [2014-10-06 00:55] 3 1829302 902736.1 0 1829302 | |
| [2014-10-06 00:55] 4 623633 225684.0 0 623633 | |
| [2014-10-06 00:55] 5 231735 56421.0 0 231735 | |
| [2014-10-06 00:55] 6 71129 14105.3 0 71129 | |
| [2014-10-06 00:55] 7 34803 3526.3 0 34803 | |
| [2014-10-06 00:55] 8 18638 881.6 0 18638 | |
| [2014-10-06 00:55] 9 14655 220.4 0 14655 | |
| [2014-10-06 00:55] 10 42305 55.1 1 13028 29277 | |
| [2014-10-06 00:55] 11 30147 13.8 1 12100 18047 | |
| [2014-10-06 00:55] 12 27542 3.4 1 16909 10633 | |
| [2014-10-06 00:55] 13 23746 0.9 1 17171 6575 | |
| [2014-10-06 00:55] 14 24842 0.9 1 19237 5605 | |
| [2014-10-06 00:55] 15 24325 0.9 1 19349 4976 | |
| [2014-10-06 00:55] 16 22560 0.9 1 17936 4624 | |
| [2014-10-06 00:55] 17 20466 0.9 1 15827 4639 | |
| [2014-10-06 00:55] 18 18262 0.9 1 14009 4253 | |
| [2014-10-06 00:55] 19 16976 0.9 1 12957 4019 | |
| [2014-10-06 00:55] 20 15535 0.9 1 11721 3814 | |
| [2014-10-06 00:55] 21 14856 0.9 1 10731 4125 | |
| [2014-10-06 00:55] 22 13582 0.9 1 9440 4142 | |
| [2014-10-06 00:55] 23 12497 0.9 1 8688 3809 | |
| [2014-10-06 00:55] 24 12231 0.9 1 8077 4154 | |
| [2014-10-06 00:55] 25 11518 0.9 1 7557 3961 | |
| [2014-10-06 00:55] 26 10429 0.9 1 6431 3998 | |
| [2014-10-06 00:55] 27 9364 0.9 1 5669 3695 | |
| [2014-10-06 00:55] 28 8874 0.9 1 5029 3845 | |
| [2014-10-06 00:55] 29 8406 0.9 1 4577 3829 | |
| [2014-10-06 00:55] 30 8292 0.9 1 4229 4063 | |
| [2014-10-06 00:55] 31 7600 0.9 1 3812 3788 | |
| [2014-10-06 00:55] 32 7392 0.9 1 3645 3747 | |
| [2014-10-06 00:55] 33 7443 0.9 1 3768 3675 | |
| [2014-10-06 00:55] 34 7150 0.9 1 3481 3669 | |
| [2014-10-06 00:55] 35 7022 0.9 1 3627 3395 | |
| [2014-10-06 00:55] 36 6885 0.9 1 3216 3669 | |
| [2014-10-06 00:55] 37 6429 0.9 1 2815 3614 | |
| [2014-10-06 00:55] 38 6358 0.9 1 2766 3592 | |
| [2014-10-06 00:55] 39 6167 0.9 1 2546 3621 | |
| [2014-10-06 00:55] 40 6326 0.9 1 2861 3465 | |
| [2014-10-06 00:55] 41 5768 0.9 1 2378 3390 | |
| [2014-10-06 00:55] 42 5916 0.9 1 2402 3514 | |
| [2014-10-06 00:55] 43 6440 0.9 1 2686 3754 | |
| [2014-10-06 00:55] 44 6409 0.9 1 2718 3691 | |
| [2014-10-06 00:55] 45 5901 0.9 1 2466 3435 | |
| [2014-10-06 00:55] 46 5878 0.9 1 2086 3792 | |
| [2014-10-06 00:55] 47 5419 0.9 1 1846 3573 | |
| [2014-10-06 00:55] 48 5719 0.9 1 1786 3933 | |
| [2014-10-06 00:55] 49 5111 0.9 1 1574 3537 | |
| [2014-10-06 00:55] 50 4912 0.9 1 1489 3423 | |
| [2014-10-06 00:55] 51 4737 0.9 1 1385 3352 | |
| [2014-10-06 00:55] 52 5120 0.9 1 1559 3561 | |
| [2014-10-06 00:55] 53 4843 0.9 1 1483 3360 | |
| [2014-10-06 00:55] 54 5488 0.9 1 1594 3894 | |
| [2014-10-06 00:55] 55 5157 0.9 1 1422 3735 | |
| [2014-10-06 00:55] 56 5048 0.9 1 1536 3512 | |
| [2014-10-06 00:55] 57 5393 0.9 1 1463 3930 | |
| [2014-10-06 00:55] 58 5065 0.9 1 1302 3763 | |
| [2014-10-06 00:55] 59 5097 0.9 1 1399 3698 | |
| [2014-10-06 00:55] 60 4826 0.9 1 1362 3464 | |
| [2014-10-06 00:55] 61 5189 0.9 1 1391 3798 | |
| [2014-10-06 00:55] 62 5256 0.9 1 1503 3753 | |
| [2014-10-06 00:55] 63 4863 0.9 1 1345 3518 | |
| [2014-10-06 00:55] 64 4748 0.9 1 1388 3360 | |
| [2014-10-06 00:55] 65 4729 0.9 1 1285 3444 | |
| [2014-10-06 00:55] 66 5152 0.9 1 1456 3696 | |
| [2014-10-06 00:55] 67 5033 0.9 1 1416 3617 | |
| [2014-10-06 00:55] 68 5398 0.9 1 1525 3873 | |
| [2014-10-06 00:55] 69 5176 0.9 1 1360 3816 | |
| [2014-10-06 00:55] 70 5002 0.9 1 1248 3754 | |
| [2014-10-06 00:55] 71 4952 0.9 1 1216 3736 | |
| [2014-10-06 00:55] 72 4970 0.9 1 1260 3710 | |
| [2014-10-06 00:55] 73 4967 0.9 1 1180 3787 | |
| [2014-10-06 00:55] 74 5339 0.9 1 1255 4084 | |
| [2014-10-06 00:55] 75 5029 0.9 1 1233 3796 | |
| [2014-10-06 00:55] 76 5193 0.9 1 1234 3959 | |
| [2014-10-06 00:55] 77 4845 0.9 1 1087 3758 | |
| [2014-10-06 00:55] 78 4711 0.9 1 1123 3588 | |
| [2014-10-06 00:55] 79 4770 0.9 1 1126 3644 | |
| [2014-10-06 00:55] 80 5159 0.9 1 1169 3990 | |
| [2014-10-06 00:55] 81 4666 0.9 1 1000 3666 | |
| [2014-10-06 00:55] 82 4842 0.9 1 1058 3784 | |
| [2014-10-06 00:55] 83 4687 0.9 1 1010 3677 | |
| [2014-10-06 00:55] 84 4431 0.9 1 1043 3388 | |
| [2014-10-06 00:55] 85 4612 0.9 1 1041 3571 | |
| [2014-10-06 00:55] 86 4785 0.9 1 1230 3555 | |
| [2014-10-06 00:55] 87 4656 0.9 1 1068 3588 | |
| [2014-10-06 00:55] 88 4367 0.9 1 997 3370 | |
| [2014-10-06 00:55] 89 4474 0.9 1 917 3557 | |
| [2014-10-06 00:55] 90 3746 0.9 1 867 2879 | |
| [2014-10-06 00:55] 91 3537 0.9 1 860 2677 | |
| [2014-10-06 00:55] 92 5929 0.9 1 1194 4735 | |
| [2014-10-06 00:55] 93 6552 0.9 1 1215 5337 | |
| [2014-10-06 00:55] 94 5833 0.9 1 962 4871 | |
| [2014-10-06 00:55] 95 3326 0.9 1 591 2735 | |
| [2014-10-06 00:55] 96 2332 0.9 1 478 1854 | |
| [2014-10-06 00:55] 97 2579 0.9 1 533 2046 | |
| [2014-10-06 00:55] 98 2738 0.9 1 510 2228 | |
| [2014-10-06 00:55] 99 2636 0.9 1 482 2154 | |
| [2014-10-06 00:55] 100 5130 0.9 1 744 4386 | |
| [2014-10-06 00:55] 101 9002 0.9 1 1164 7838 | |
| [2014-10-06 00:55] | |
| [2014-10-06 00:55] === Adapter 2 === | |
| [2014-10-06 00:55] | |
| [2014-10-06 00:55] Adapter 'TTTTTTTTTTTTT', length 13, was trimmed 3767052 times. | |
| [2014-10-06 00:55] | |
| [2014-10-06 00:55] No. of allowed errors: | |
| [2014-10-06 00:55] 0-9 bp: 0; 10-13 bp: 1 | |
| [2014-10-06 00:55] | |
| [2014-10-06 00:55] Overview of removed sequences | |
| [2014-10-06 00:55] length count expect max.err error counts | |
| [2014-10-06 00:55] 3 1855222 902736.1 0 1855222 | |
| [2014-10-06 00:55] 4 652123 225684.0 0 652123 | |
| [2014-10-06 00:55] 5 233204 56421.0 0 233204 | |
| [2014-10-06 00:55] 6 76754 14105.3 0 76754 | |
| [2014-10-06 00:55] 7 45993 3526.3 0 45993 | |
| [2014-10-06 00:55] 8 17454 881.6 0 17454 | |
| [2014-10-06 00:55] 9 14376 220.4 0 14376 | |
| [2014-10-06 00:55] 10 45477 55.1 1 13075 32402 | |
| [2014-10-06 00:55] 11 34083 13.8 1 12810 21273 | |
| [2014-10-06 00:55] 12 34903 3.4 1 21510 13393 | |
| [2014-10-06 00:55] 13 33416 0.9 1 24416 9000 | |
| [2014-10-06 00:55] 14 37496 0.9 1 29646 7850 | |
| [2014-10-06 00:55] 15 39056 0.9 1 32498 6558 | |
| [2014-10-06 00:55] 16 36981 0.9 1 31418 5563 | |
| [2014-10-06 00:55] 17 32874 0.9 1 27535 5339 | |
| [2014-10-06 00:55] 18 28379 0.9 1 23045 5334 | |
| [2014-10-06 00:55] 19 25101 0.9 1 20139 4962 | |
| [2014-10-06 00:55] 20 25774 0.9 1 17181 8593 | |
| [2014-10-06 00:55] 21 20282 0.9 1 15460 4822 | |
| [2014-10-06 00:55] 22 17301 0.9 1 12730 4571 | |
| [2014-10-06 00:55] 23 15578 0.9 1 10979 4599 | |
| [2014-10-06 00:55] 24 14605 0.9 1 9578 5027 | |
| [2014-10-06 00:55] 25 13287 0.9 1 8063 5224 | |
| [2014-10-06 00:55] 26 11023 0.9 1 6782 4241 | |
| [2014-10-06 00:55] 27 10192 0.9 1 6044 4148 | |
| [2014-10-06 00:55] 28 9718 0.9 1 5302 4416 | |
| [2014-10-06 00:55] 29 9391 0.9 1 4855 4536 | |
| [2014-10-06 00:55] 30 8658 0.9 1 4254 4404 | |
| [2014-10-06 00:55] 31 7661 0.9 1 3573 4088 | |
| [2014-10-06 00:55] 32 7337 0.9 1 3192 4145 | |
| [2014-10-06 00:55] 33 7337 0.9 1 3112 4225 | |
| [2014-10-06 00:55] 34 6565 0.9 1 2616 3949 | |
| [2014-10-06 00:55] 35 6227 0.9 1 2374 3853 | |
| [2014-10-06 00:55] 36 6503 0.9 1 2265 4238 | |
| [2014-10-06 00:55] 37 6149 0.9 1 2160 3989 | |
| [2014-10-06 00:55] 38 6029 0.9 1 2097 3932 | |
| [2014-10-06 00:55] 39 6237 0.9 1 2129 4108 | |
| [2014-10-06 00:55] 40 6043 0.9 1 1922 4121 | |
| [2014-10-06 00:55] 41 5914 0.9 1 1856 4058 | |
| [2014-10-06 00:55] 42 6091 0.9 1 1890 4201 | |
| [2014-10-06 00:55] 43 6218 0.9 1 1786 4432 | |
| [2014-10-06 00:55] 44 5689 0.9 1 1825 3864 | |
| [2014-10-06 00:55] 45 6149 0.9 1 1941 4208 | |
| [2014-10-06 00:55] 46 5813 0.9 1 1825 3988 | |
| [2014-10-06 00:55] 47 5687 0.9 1 1762 3925 | |
| [2014-10-06 00:55] 48 5806 0.9 1 1598 4208 | |
| [2014-10-06 00:55] 49 5828 0.9 1 1449 4379 | |
| [2014-10-06 00:55] 50 5592 0.9 1 1448 4144 | |
| [2014-10-06 00:55] 51 5033 0.9 1 1324 3709 | |
| [2014-10-06 00:55] 52 4952 0.9 1 1215 3737 | |
| [2014-10-06 00:55] 53 4749 0.9 1 1205 3544 | |
| [2014-10-06 00:55] 54 5084 0.9 1 1223 3861 | |
| [2014-10-06 00:55] 55 4897 0.9 1 1345 3552 | |
| [2014-10-06 00:55] 56 5207 0.9 1 1361 3846 | |
| [2014-10-06 00:55] 57 5019 0.9 1 1170 3849 | |
| [2014-10-06 00:55] 58 4938 0.9 1 1058 3880 | |
| [2014-10-06 00:55] 59 5116 0.9 1 1170 3946 | |
| [2014-10-06 00:55] 60 4756 0.9 1 1041 3715 | |
| [2014-10-06 00:55] 61 5040 0.9 1 1164 3876 | |
| [2014-10-06 00:55] 62 4576 0.9 1 1025 3551 | |
| [2014-10-06 00:55] 63 4539 0.9 1 1039 3500 | |
| [2014-10-06 00:55] 64 4599 0.9 1 1020 3579 | |
| [2014-10-06 00:55] 65 4664 0.9 1 1044 3620 | |
| [2014-10-06 00:55] 66 4739 0.9 1 943 3796 | |
| [2014-10-06 00:55] 67 4571 0.9 1 1039 3532 | |
| [2014-10-06 00:55] 68 4739 0.9 1 998 3741 | |
| [2014-10-06 00:55] 69 4822 0.9 1 1079 3743 | |
| [2014-10-06 00:55] 70 4868 0.9 1 996 3872 | |
| [2014-10-06 00:55] 71 4576 0.9 1 910 3666 | |
| [2014-10-06 00:55] 72 5036 0.9 1 974 4062 | |
| [2014-10-06 00:55] 73 4501 0.9 1 887 3614 | |
| [2014-10-06 00:55] 74 4342 0.9 1 920 3422 | |
| [2014-10-06 00:55] 75 4476 0.9 1 929 3547 | |
| [2014-10-06 00:55] 76 4385 0.9 1 864 3521 | |
| [2014-10-06 00:55] 77 4783 0.9 1 840 3943 | |
| [2014-10-06 00:55] 78 4519 0.9 1 915 3604 | |
| [2014-10-06 00:55] 79 4511 0.9 1 959 3552 | |
| [2014-10-06 00:55] 80 4806 0.9 1 883 3923 | |
| [2014-10-06 00:55] 81 4822 0.9 1 839 3983 | |
| [2014-10-06 00:55] 82 4635 0.9 1 849 3786 | |
| [2014-10-06 00:55] 83 4222 0.9 1 751 3471 | |
| [2014-10-06 00:55] 84 4370 0.9 1 796 3574 | |
| [2014-10-06 00:55] 85 4228 0.9 1 783 3445 | |
| [2014-10-06 00:55] 86 4550 0.9 1 861 3689 | |
| [2014-10-06 00:55] 87 4221 0.9 1 750 3471 | |
| [2014-10-06 00:55] 88 4531 0.9 1 719 3812 | |
| [2014-10-06 00:55] 89 4459 0.9 1 774 3685 | |
| [2014-10-06 00:55] 90 6153 0.9 1 878 5275 | |
| [2014-10-06 00:55] 91 5202 0.9 1 802 4400 | |
| [2014-10-06 00:55] 92 4891 0.9 1 727 4164 | |
| [2014-10-06 00:55] 93 4532 0.9 1 803 3729 | |
| [2014-10-06 00:55] 94 3057 0.9 1 546 2511 | |
| [2014-10-06 00:55] 95 4070 0.9 1 631 3439 | |
| [2014-10-06 00:55] 96 3786 0.9 1 565 3221 | |
| [2014-10-06 00:55] 97 3641 0.9 1 520 3121 | |
| [2014-10-06 00:55] 98 2555 0.9 1 391 2164 | |
| [2014-10-06 00:55] 99 2706 0.9 1 480 2226 | |
| [2014-10-06 00:55] 100 9170 0.9 1 902 8268 | |
| [2014-10-06 00:55] 101 10832 0.9 1 1708 9124 | |
| [2014-10-06 00:55] | |
| [2014-10-06 00:55] === Adapter 3 === | |
| [2014-10-06 00:55] | |
| [2014-10-06 00:55] Adapter 'AGATCGGAAGAG', length 12, was trimmed 5893166 times. | |
| [2014-10-06 00:55] | |
| [2014-10-06 00:55] No. of allowed errors: | |
| [2014-10-06 00:55] 0-9 bp: 0; 10-12 bp: 1 | |
| [2014-10-06 00:55] | |
| [2014-10-06 00:55] Overview of removed sequences | |
| [2014-10-06 00:55] length count expect max.err error counts | |
| [2014-10-06 00:55] 3 2433755 902736.1 0 2433755 | |
| [2014-10-06 00:55] 4 706971 225684.0 0 706971 | |
| [2014-10-06 00:55] 5 314084 56421.0 0 314084 | |
| [2014-10-06 00:55] 6 263272 14105.3 0 263272 | |
| [2014-10-06 00:55] 7 208325 3526.3 0 208325 | |
| [2014-10-06 00:55] 8 208898 881.6 0 208898 | |
| [2014-10-06 00:55] 9 172401 220.4 0 169495 2906 | |
| [2014-10-06 00:55] 10 152733 55.1 1 147351 5382 | |
| [2014-10-06 00:55] 11 111637 13.8 1 106796 4841 | |
| [2014-10-06 00:55] 12 114360 3.4 1 111164 3196 | |
| [2014-10-06 00:55] 13 94598 3.4 1 91579 3019 | |
| [2014-10-06 00:55] 14 108089 3.4 1 105381 2708 | |
| [2014-10-06 00:55] 15 62772 3.4 1 60903 1869 | |
| [2014-10-06 00:55] 16 72553 3.4 1 70235 2318 | |
| [2014-10-06 00:55] 17 86450 3.4 1 84259 2191 | |
| [2014-10-06 00:55] 18 52326 3.4 1 50809 1517 | |
| [2014-10-06 00:55] 19 57743 3.4 1 56229 1514 | |
| [2014-10-06 00:55] 20 48107 3.4 1 46882 1225 | |
| [2014-10-06 00:55] 21 20094 3.4 1 19175 919 | |
| [2014-10-06 00:55] 22 28768 3.4 1 27769 999 | |
| [2014-10-06 00:55] 23 28564 3.4 1 26186 2378 | |
| [2014-10-06 00:55] 24 30643 3.4 1 29223 1420 | |
| [2014-10-06 00:55] 25 23894 3.4 1 22492 1402 | |
| [2014-10-06 00:55] 26 27982 3.4 1 22097 5885 | |
| [2014-10-06 00:55] 27 18731 3.4 1 16654 2077 | |
| [2014-10-06 00:55] 28 25961 3.4 1 24130 1831 | |
| [2014-10-06 00:55] 29 17395 3.4 1 15071 2324 | |
| [2014-10-06 00:55] 30 29509 3.4 1 28154 1355 | |
| [2014-10-06 00:55] 31 7626 3.4 1 6139 1487 | |
| [2014-10-06 00:55] 32 10708 3.4 1 9914 794 | |
| [2014-10-06 00:55] 33 6260 3.4 1 5357 903 | |
| [2014-10-06 00:55] 34 8049 3.4 1 7119 930 | |
| [2014-10-06 00:55] 35 8131 3.4 1 7180 951 | |
| [2014-10-06 00:55] 36 9024 3.4 1 8038 986 | |
| [2014-10-06 00:55] 37 9906 3.4 1 6973 2933 | |
| [2014-10-06 00:55] 38 8950 3.4 1 7842 1108 | |
| [2014-10-06 00:55] 39 9646 3.4 1 8444 1202 | |
| [2014-10-06 00:55] 40 10089 3.4 1 8995 1094 | |
| [2014-10-06 00:55] 41 10695 3.4 1 8222 2473 | |
| [2014-10-06 00:55] 42 15096 3.4 1 13612 1484 | |
| [2014-10-06 00:55] 43 4131 3.4 1 3261 870 | |
| [2014-10-06 00:55] 44 9537 3.4 1 7586 1951 | |
| [2014-10-06 00:55] 45 8902 3.4 1 8003 899 | |
| [2014-10-06 00:55] 46 3124 3.4 1 2390 734 | |
| [2014-10-06 00:55] 47 4527 3.4 1 3878 649 | |
| [2014-10-06 00:55] 48 5002 3.4 1 4321 681 | |
| [2014-10-06 00:55] 49 5575 3.4 1 4085 1490 | |
| [2014-10-06 00:55] 50 17497 3.4 1 16059 1438 | |
| [2014-10-06 00:55] 51 5159 3.4 1 4236 923 | |
| [2014-10-06 00:55] 52 5267 3.4 1 4741 526 | |
| [2014-10-06 00:55] 53 2561 3.4 1 1858 703 | |
| [2014-10-06 00:55] 54 3107 3.4 1 2130 977 | |
| [2014-10-06 00:55] 55 2972 3.4 1 2202 770 | |
| [2014-10-06 00:55] 56 2947 3.4 1 1966 981 | |
| [2014-10-06 00:55] 57 4746 3.4 1 2197 2549 | |
| [2014-10-06 00:55] 58 4011 3.4 1 2562 1449 | |
| [2014-10-06 00:55] 59 4000 3.4 1 2517 1483 | |
| [2014-10-06 00:55] 60 7184 3.4 1 4793 2391 | |
| [2014-10-06 00:55] 61 6080 3.4 1 2371 3709 | |
| [2014-10-06 00:55] 62 10767 3.4 1 3601 7166 | |
| [2014-10-06 00:55] 63 14178 3.4 1 4173 10005 | |
| [2014-10-06 00:55] 64 29007 3.4 1 5843 23164 | |
| [2014-10-06 00:55] 65 46597 3.4 1 5632 40965 | |
| [2014-10-06 00:55] 66 23842 3.4 1 4841 19001 | |
| [2014-10-06 00:55] 67 11117 3.4 1 1423 9694 | |
| [2014-10-06 00:55] 68 1486 3.4 1 870 616 | |
| [2014-10-06 00:55] 69 632 3.4 1 263 369 | |
| [2014-10-06 00:55] 70 366 3.4 1 20 346 | |
| [2014-10-06 00:55] 71 369 3.4 1 8 361 | |
| [2014-10-06 00:55] 72 347 3.4 1 4 343 | |
| [2014-10-06 00:55] 73 316 3.4 1 7 309 | |
| [2014-10-06 00:55] 74 348 3.4 1 10 338 | |
| [2014-10-06 00:55] 75 366 3.4 1 13 353 | |
| [2014-10-06 00:55] 76 353 3.4 1 10 343 | |
| [2014-10-06 00:55] 77 463 3.4 1 18 445 | |
| [2014-10-06 00:55] 78 343 3.4 1 10 333 | |
| [2014-10-06 00:55] 79 369 3.4 1 16 353 | |
| [2014-10-06 00:55] 80 307 3.4 1 9 298 | |
| [2014-10-06 00:55] 81 367 3.4 1 4 363 | |
| [2014-10-06 00:55] 82 428 3.4 1 16 412 | |
| [2014-10-06 00:55] 83 390 3.4 1 16 374 | |
| [2014-10-06 00:55] 84 419 3.4 1 4 415 | |
| [2014-10-06 00:55] 85 338 3.4 1 10 328 | |
| [2014-10-06 00:55] 86 376 3.4 1 6 370 | |
| [2014-10-06 00:55] 87 287 3.4 1 8 279 | |
| [2014-10-06 00:55] 88 314 3.4 1 11 303 | |
| [2014-10-06 00:55] 89 309 3.4 1 13 296 | |
| [2014-10-06 00:55] 90 303 3.4 1 8 295 | |
| [2014-10-06 00:55] 91 397 3.4 1 14 383 | |
| [2014-10-06 00:55] 92 552 3.4 1 8 544 | |
| [2014-10-06 00:55] 93 380 3.4 1 26 354 | |
| [2014-10-06 00:55] 94 283 3.4 1 14 269 | |
| [2014-10-06 00:55] 95 255 3.4 1 22 233 | |
| [2014-10-06 00:55] 96 371 3.4 1 8 363 | |
| [2014-10-06 00:55] 97 269 3.4 1 24 245 | |
| [2014-10-06 00:55] 98 999 3.4 1 50 949 | |
| [2014-10-06 00:55] 99 352 3.4 1 12 340 | |
| [2014-10-06 00:55] 100 206 3.4 1 14 192 | |
| [2014-10-06 00:55] 101 2874 3.4 1 214 2660 | |
| [2014-10-06 00:55] | |
| [2014-10-06 00:55] === Adapter 4 === | |
| [2014-10-06 00:55] | |
| [2014-10-06 00:55] Adapter 'CTCTTCCGATCT', length 12, was trimmed 3147724 times. | |
| [2014-10-06 00:55] | |
| [2014-10-06 00:55] No. of allowed errors: | |
| [2014-10-06 00:55] 0-9 bp: 0; 10-12 bp: 1 | |
| [2014-10-06 00:55] | |
| [2014-10-06 00:55] Overview of removed sequences | |
| [2014-10-06 00:55] length count expect max.err error counts | |
| [2014-10-06 00:55] 3 2257939 902736.1 0 2257939 | |
| [2014-10-06 00:55] 4 575209 225684.0 0 575209 | |
| [2014-10-06 00:55] 5 174987 56421.0 0 174987 | |
| [2014-10-06 00:55] 6 61453 14105.3 0 61453 | |
| [2014-10-06 00:55] 7 22181 3526.3 0 22181 | |
| [2014-10-06 00:55] 8 1037 881.6 0 1037 | |
| [2014-10-06 00:55] 9 2299 220.4 0 218 2081 | |
| [2014-10-06 00:55] 10 16824 55.1 1 173 16651 | |
| [2014-10-06 00:55] 11 1511 13.8 1 79 1432 | |
| [2014-10-06 00:55] 12 426 3.4 1 70 356 | |
| [2014-10-06 00:55] 13 319 3.4 1 47 272 | |
| [2014-10-06 00:55] 14 344 3.4 1 52 292 | |
| [2014-10-06 00:55] 15 327 3.4 1 33 294 | |
| [2014-10-06 00:55] 16 314 3.4 1 24 290 | |
| [2014-10-06 00:55] 17 308 3.4 1 22 286 | |
| [2014-10-06 00:55] 18 288 3.4 1 16 272 | |
| [2014-10-06 00:55] 19 249 3.4 1 12 237 | |
| [2014-10-06 00:55] 20 333 3.4 1 16 317 | |
| [2014-10-06 00:55] 21 315 3.4 1 10 305 | |
| [2014-10-06 00:55] 22 458 3.4 1 20 438 | |
| [2014-10-06 00:55] 23 422 3.4 1 10 412 | |
| [2014-10-06 00:55] 24 391 3.4 1 16 375 | |
| [2014-10-06 00:55] 25 373 3.4 1 10 363 | |
| [2014-10-06 00:55] 26 380 3.4 1 12 368 | |
| [2014-10-06 00:55] 27 327 3.4 1 9 318 | |
| [2014-10-06 00:55] 28 370 3.4 1 6 364 | |
| [2014-10-06 00:55] 29 480 3.4 1 12 468 | |
| [2014-10-06 00:55] 30 390 3.4 1 16 374 | |
| [2014-10-06 00:55] 31 407 3.4 1 15 392 | |
| [2014-10-06 00:55] 32 567 3.4 1 12 555 | |
| [2014-10-06 00:55] 33 463 3.4 1 8 455 | |
| [2014-10-06 00:55] 34 501 3.4 1 13 488 | |
| [2014-10-06 00:55] 35 479 3.4 1 16 463 | |
| [2014-10-06 00:55] 36 332 3.4 1 8 324 | |
| [2014-10-06 00:55] 37 443 3.4 1 11 432 | |
| [2014-10-06 00:55] 38 304 3.4 1 18 286 | |
| [2014-10-06 00:55] 39 318 3.4 1 23 295 | |
| [2014-10-06 00:55] 40 344 3.4 1 25 319 | |
| [2014-10-06 00:55] 41 267 3.4 1 12 255 | |
| [2014-10-06 00:55] 42 309 3.4 1 8 301 | |
| [2014-10-06 00:55] 43 312 3.4 1 23 289 | |
| [2014-10-06 00:55] 44 373 3.4 1 17 356 | |
| [2014-10-06 00:55] 45 462 3.4 1 8 454 | |
| [2014-10-06 00:55] 46 419 3.4 1 21 398 | |
| [2014-10-06 00:55] 47 501 3.4 1 28 473 | |
| [2014-10-06 00:55] 48 323 3.4 1 14 309 | |
| [2014-10-06 00:55] 49 496 3.4 1 122 374 | |
| [2014-10-06 00:55] 50 275 3.4 1 6 269 | |
| [2014-10-06 00:55] 51 349 3.4 1 6 343 | |
| [2014-10-06 00:55] 52 390 3.4 1 4 386 | |
| [2014-10-06 00:55] 53 406 3.4 1 12 394 | |
| [2014-10-06 00:55] 54 388 3.4 1 12 376 | |
| [2014-10-06 00:55] 55 367 3.4 1 16 351 | |
| [2014-10-06 00:55] 56 367 3.4 1 14 353 | |
| [2014-10-06 00:55] 57 315 3.4 1 0 315 | |
| [2014-10-06 00:55] 58 397 3.4 1 4 393 | |
| [2014-10-06 00:55] 59 286 3.4 1 5 281 | |
| [2014-10-06 00:55] 60 277 3.4 1 2 275 | |
| [2014-10-06 00:55] 61 323 3.4 1 4 319 | |
| [2014-10-06 00:55] 62 358 3.4 1 0 358 | |
| [2014-10-06 00:55] 63 324 3.4 1 4 320 | |
| [2014-10-06 00:55] 64 372 3.4 1 0 372 | |
| [2014-10-06 00:55] 65 322 3.4 1 8 314 | |
| [2014-10-06 00:55] 66 252 3.4 1 4 248 | |
| [2014-10-06 00:55] 67 301 3.4 1 8 293 | |
| [2014-10-06 00:55] 68 331 3.4 1 2 329 | |
| [2014-10-06 00:55] 69 320 3.4 1 13 307 | |
| [2014-10-06 00:55] 70 276 3.4 1 6 270 | |
| [2014-10-06 00:55] 71 345 3.4 1 3 342 | |
| [2014-10-06 00:55] 72 282 3.4 1 6 276 | |
| [2014-10-06 00:55] 73 308 3.4 1 5 303 | |
| [2014-10-06 00:55] 74 388 3.4 1 10 378 | |
| [2014-10-06 00:55] 75 455 3.4 1 19 436 | |
| [2014-10-06 00:55] 76 345 3.4 1 6 339 | |
| [2014-10-06 00:55] 77 318 3.4 1 6 312 | |
| [2014-10-06 00:55] 78 317 3.4 1 12 305 | |
| [2014-10-06 00:55] 79 372 3.4 1 2 370 | |
| [2014-10-06 00:55] 80 229 3.4 1 8 221 | |
| [2014-10-06 00:55] 81 352 3.4 1 12 340 | |
| [2014-10-06 00:55] 82 411 3.4 1 2 409 | |
| [2014-10-06 00:55] 83 476 3.4 1 2 474 | |
| [2014-10-06 00:55] 84 342 3.4 1 6 336 | |
| [2014-10-06 00:55] 85 377 3.4 1 20 357 | |
| [2014-10-06 00:55] 86 311 3.4 1 8 303 | |
| [2014-10-06 00:55] 87 422 3.4 1 6 416 | |
| [2014-10-06 00:55] 88 341 3.4 1 14 327 | |
| [2014-10-06 00:55] 89 405 3.4 1 22 383 | |
| [2014-10-06 00:55] 90 398 3.4 1 20 378 | |
| [2014-10-06 00:55] 91 493 3.4 1 50 443 | |
| [2014-10-06 00:55] 92 351 3.4 1 16 335 | |
| [2014-10-06 00:55] 93 506 3.4 1 48 458 | |
| [2014-10-06 00:55] 94 823 3.4 1 122 701 | |
| [2014-10-06 00:55] 95 350 3.4 1 38 312 | |
| [2014-10-06 00:55] 96 866 3.4 1 102 764 | |
| [2014-10-06 00:55] 97 304 3.4 1 38 266 | |
| [2014-10-06 00:55] 98 779 3.4 1 250 529 | |
| [2014-10-06 00:55] 99 622 3.4 1 60 562 | |
| [2014-10-06 00:55] 100 236 3.4 1 50 186 | |
| [2014-10-06 00:55] 101 330 3.4 1 22 308 | |
| [2014-10-06 00:55] | |
| [2014-10-06 02:01] cutadapt version 1.4.2 | |
| [2014-10-06 02:01] Command line parameters: --times=2 --quality-base=33 --quality-cutoff=5 --format=fastq --adapter=AAAAAAAAAAAAA --adapter=TTTTTTTTTTTTT --adapter=AGATCGGAAGAG --adapter=CTCTTCCGATCT --minimum-length=25 -o /vagrant_data/seqc-test/seqc/work/trimmed/SRR950083_2.trimmed.fastq.gz -p /vagrant_data/seqc-test/seqc/work/trimmed/SRR950083_1.trimmed.fastq.gz /vagrant_data/seqc-test/seqc/work/trimmed/SRR950083_2.trimmed.tmp.fastq.gz /vagrant_data/seqc-test/seqc/work/trimmed/SRR950083_1.trimmed.tmp.fastq.gz | |
| [2014-10-06 02:01] Maximum error rate: 10.00% | |
| [2014-10-06 02:01] No. of adapters: 4 | |
| [2014-10-06 02:01] Processed reads: 103563709 | |
| [2014-10-06 02:01] Processed bases: 10459934609 bp (10459.9 Mbp) | |
| [2014-10-06 02:01] Trimmed reads: 13533867 (13.1%) | |
| [2014-10-06 02:01] Quality-trimmed: 381663069 bp (381.7 Mbp) (3.65% of total) | |
| [2014-10-06 02:01] Trimmed bases: 234261850 bp (234.3 Mbp) (2.24% of total) | |
| [2014-10-06 02:01] Too short reads: 1724426 (1.7% of processed reads) | |
| [2014-10-06 02:01] Too long reads: 0 (0.0% of processed reads) | |
| [2014-10-06 02:01] Total time: 4853.65 s | |
| [2014-10-06 02:01] Time per read: 0.047 ms | |
| [2014-10-06 02:01] | |
| [2014-10-06 02:01] === Adapter 1 === | |
| [2014-10-06 02:01] | |
| [2014-10-06 02:01] Adapter 'AAAAAAAAAAAAA', length 13, was trimmed 6617796 times. | |
| [2014-10-06 02:01] | |
| [2014-10-06 02:01] No. of allowed errors: | |
| [2014-10-06 02:01] 0-9 bp: 0; 10-13 bp: 1 | |
| [2014-10-06 02:01] | |
| [2014-10-06 02:01] Overview of removed sequences | |
| [2014-10-06 02:01] length count expect max.err error counts | |
| [2014-10-06 02:01] 3 3362772 1618183.0 0 3362772 | |
| [2014-10-06 02:01] 4 1152619 404545.7 0 1152619 | |
| [2014-10-06 02:01] 5 435666 101136.4 0 435666 | |
| [2014-10-06 02:01] 6 140953 25284.1 0 140953 | |
| [2014-10-06 02:01] 7 65350 6321.0 0 65350 | |
| [2014-10-06 02:01] 8 30746 1580.3 0 30746 | |
| [2014-10-06 02:01] 9 24773 395.1 0 24773 | |
| [2014-10-06 02:01] 10 81145 98.8 1 22149 58996 | |
| [2014-10-06 02:01] 11 57724 24.7 1 21504 36220 | |
| [2014-10-06 02:01] 12 54318 6.2 1 32322 21996 | |
| [2014-10-06 02:01] 13 46119 1.5 1 33329 12790 | |
| [2014-10-06 02:01] 14 46383 1.5 1 35682 10701 | |
| [2014-10-06 02:01] 15 45415 1.5 1 35267 10148 | |
| [2014-10-06 02:01] 16 42313 1.5 1 32661 9652 | |
| [2014-10-06 02:01] 17 37492 1.5 1 28831 8661 | |
| [2014-10-06 02:01] 18 36229 1.5 1 25350 10879 | |
| [2014-10-06 02:01] 19 30871 1.5 1 22874 7997 | |
| [2014-10-06 02:01] 20 29446 1.5 1 21331 8115 | |
| [2014-10-06 02:01] 21 27398 1.5 1 19583 7815 | |
| [2014-10-06 02:01] 22 24901 1.5 1 17276 7625 | |
| [2014-10-06 02:01] 23 23253 1.5 1 15383 7870 | |
| [2014-10-06 02:01] 24 21764 1.5 1 13781 7983 | |
| [2014-10-06 02:01] 25 19542 1.5 1 12124 7418 | |
| [2014-10-06 02:01] 26 19213 1.5 1 11391 7822 | |
| [2014-10-06 02:01] 27 17021 1.5 1 9841 7180 | |
| [2014-10-06 02:01] 28 16393 1.5 1 8940 7453 | |
| [2014-10-06 02:01] 29 15316 1.5 1 8368 6948 | |
| [2014-10-06 02:01] 30 15265 1.5 1 7766 7499 | |
| [2014-10-06 02:01] 31 14910 1.5 1 7229 7681 | |
| [2014-10-06 02:01] 32 14137 1.5 1 6830 7307 | |
| [2014-10-06 02:01] 33 13760 1.5 1 6571 7189 | |
| [2014-10-06 02:01] 34 13913 1.5 1 6547 7366 | |
| [2014-10-06 02:01] 35 12939 1.5 1 6351 6588 | |
| [2014-10-06 02:01] 36 12886 1.5 1 5761 7125 | |
| [2014-10-06 02:01] 37 12458 1.5 1 5470 6988 | |
| [2014-10-06 02:01] 38 11957 1.5 1 4959 6998 | |
| [2014-10-06 02:01] 39 11977 1.5 1 4897 7080 | |
| [2014-10-06 02:01] 40 11740 1.5 1 5061 6679 | |
| [2014-10-06 02:01] 41 11383 1.5 1 4477 6906 | |
| [2014-10-06 02:01] 42 10989 1.5 1 4261 6728 | |
| [2014-10-06 02:01] 43 11079 1.5 1 4495 6584 | |
| [2014-10-06 02:01] 44 11678 1.5 1 4562 7116 | |
| [2014-10-06 02:01] 45 10573 1.5 1 4250 6323 | |
| [2014-10-06 02:01] 46 10331 1.5 1 3645 6686 | |
| [2014-10-06 02:01] 47 10392 1.5 1 3525 6867 | |
| [2014-10-06 02:01] 48 10618 1.5 1 3534 7084 | |
| [2014-10-06 02:01] 49 10050 1.5 1 3153 6897 | |
| [2014-10-06 02:01] 50 9666 1.5 1 2929 6737 | |
| [2014-10-06 02:01] 51 9401 1.5 1 2875 6526 | |
| [2014-10-06 02:01] 52 9398 1.5 1 3019 6379 | |
| [2014-10-06 02:01] 53 9204 1.5 1 2956 6248 | |
| [2014-10-06 02:01] 54 9711 1.5 1 2904 6807 | |
| [2014-10-06 02:01] 55 9661 1.5 1 2818 6843 | |
| [2014-10-06 02:01] 56 9226 1.5 1 2744 6482 | |
| [2014-10-06 02:01] 57 9419 1.5 1 2582 6837 | |
| [2014-10-06 02:01] 58 8938 1.5 1 2472 6466 | |
| [2014-10-06 02:01] 59 8811 1.5 1 2623 6188 | |
| [2014-10-06 02:01] 60 9373 1.5 1 2680 6693 | |
| [2014-10-06 02:01] 61 9558 1.5 1 2865 6693 | |
| [2014-10-06 02:01] 62 9886 1.5 1 2984 6902 | |
| [2014-10-06 02:01] 63 9240 1.5 1 2723 6517 | |
| [2014-10-06 02:01] 64 9318 1.5 1 2675 6643 | |
| [2014-10-06 02:01] 65 8849 1.5 1 2424 6425 | |
| [2014-10-06 02:01] 66 9278 1.5 1 2578 6700 | |
| [2014-10-06 02:01] 67 9325 1.5 1 2648 6677 | |
| [2014-10-06 02:01] 68 8882 1.5 1 2630 6252 | |
| [2014-10-06 02:01] 69 9410 1.5 1 2528 6882 | |
| [2014-10-06 02:01] 70 9061 1.5 1 2255 6806 | |
| [2014-10-06 02:01] 71 9779 1.5 1 2186 7593 | |
| [2014-10-06 02:01] 72 9911 1.5 1 2357 7554 | |
| [2014-10-06 02:01] 73 9646 1.5 1 2239 7407 | |
| [2014-10-06 02:01] 74 9537 1.5 1 2406 7131 | |
| [2014-10-06 02:01] 75 9075 1.5 1 2186 6889 | |
| [2014-10-06 02:01] 76 9667 1.5 1 2326 7341 | |
| [2014-10-06 02:01] 77 9176 1.5 1 2106 7070 | |
| [2014-10-06 02:01] 78 9159 1.5 1 2059 7100 | |
| [2014-10-06 02:01] 79 8908 1.5 1 2055 6853 | |
| [2014-10-06 02:01] 80 9168 1.5 1 1972 7196 | |
| [2014-10-06 02:01] 81 9346 1.5 1 2154 7192 | |
| [2014-10-06 02:01] 82 9375 1.5 1 2114 7261 | |
| [2014-10-06 02:01] 83 8669 1.5 1 1920 6749 | |
| [2014-10-06 02:01] 84 8682 1.5 1 2025 6657 | |
| [2014-10-06 02:01] 85 8731 1.5 1 1861 6870 | |
| [2014-10-06 02:01] 86 9127 1.5 1 2166 6961 | |
| [2014-10-06 02:01] 87 8708 1.5 1 1957 6751 | |
| [2014-10-06 02:01] 88 8368 1.5 1 1826 6542 | |
| [2014-10-06 02:01] 89 8293 1.5 1 1671 6622 | |
| [2014-10-06 02:01] 90 6842 1.5 1 1595 5247 | |
| [2014-10-06 02:01] 91 6290 1.5 1 1530 4760 | |
| [2014-10-06 02:01] 92 10707 1.5 1 2231 8476 | |
| [2014-10-06 02:01] 93 12053 1.5 1 2287 9766 | |
| [2014-10-06 02:01] 94 11221 1.5 1 1735 9486 | |
| [2014-10-06 02:01] 95 5725 1.5 1 1036 4689 | |
| [2014-10-06 02:01] 96 4167 1.5 1 827 3340 | |
| [2014-10-06 02:01] 97 4966 1.5 1 871 4095 | |
| [2014-10-06 02:01] 98 4771 1.5 1 925 3846 | |
| [2014-10-06 02:01] 99 5772 1.5 1 948 4824 | |
| [2014-10-06 02:01] 100 10010 1.5 1 1356 8654 | |
| [2014-10-06 02:01] 101 18162 1.5 1 2250 15912 | |
| [2014-10-06 02:01] | |
| [2014-10-06 02:01] === Adapter 2 === | |
| [2014-10-06 02:01] | |
| [2014-10-06 02:01] Adapter 'TTTTTTTTTTTTT', length 13, was trimmed 6888893 times. | |
| [2014-10-06 02:01] | |
| [2014-10-06 02:01] No. of allowed errors: | |
| [2014-10-06 02:01] 0-9 bp: 0; 10-13 bp: 1 | |
| [2014-10-06 02:01] | |
| [2014-10-06 02:01] Overview of removed sequences | |
| [2014-10-06 02:01] length count expect max.err error counts | |
| [2014-10-06 02:01] 3 3405650 1618183.0 0 3405650 | |
| [2014-10-06 02:01] 4 1199782 404545.7 0 1199782 | |
| [2014-10-06 02:01] 5 415289 101136.4 0 415289 | |
| [2014-10-06 02:01] 6 141759 25284.1 0 141759 | |
| [2014-10-06 02:01] 7 82401 6321.0 0 82401 | |
| [2014-10-06 02:01] 8 29454 1580.3 0 29454 | |
| [2014-10-06 02:01] 9 25099 395.1 0 25099 | |
| [2014-10-06 02:01] 10 84351 98.8 1 22945 61406 | |
| [2014-10-06 02:01] 11 60556 24.7 1 22719 37837 | |
| [2014-10-06 02:01] 12 63736 6.2 1 37858 25878 | |
| [2014-10-06 02:01] 13 58621 1.5 1 41873 16748 | |
| [2014-10-06 02:01] 14 63481 1.5 1 49409 14072 | |
| [2014-10-06 02:01] 15 66401 1.5 1 53841 12560 | |
| [2014-10-06 02:01] 16 63079 1.5 1 52375 10704 | |
| [2014-10-06 02:01] 17 55056 1.5 1 44891 10165 | |
| [2014-10-06 02:01] 18 46789 1.5 1 37514 9275 | |
| [2014-10-06 02:01] 19 42717 1.5 1 33205 9512 | |
| [2014-10-06 02:01] 20 41887 1.5 1 29684 12203 | |
| [2014-10-06 02:01] 21 34849 1.5 1 25511 9338 | |
| [2014-10-06 02:01] 22 31233 1.5 1 22002 9231 | |
| [2014-10-06 02:01] 23 28397 1.5 1 19324 9073 | |
| [2014-10-06 02:01] 24 26193 1.5 1 16682 9511 | |
| [2014-10-06 02:01] 25 23452 1.5 1 14400 9052 | |
| [2014-10-06 02:01] 26 21212 1.5 1 12382 8830 | |
| [2014-10-06 02:01] 27 19128 1.5 1 11073 8055 | |
| [2014-10-06 02:01] 28 18030 1.5 1 9566 8464 | |
| [2014-10-06 02:01] 29 16405 1.5 1 8343 8062 | |
| [2014-10-06 02:01] 30 15634 1.5 1 7620 8014 | |
| [2014-10-06 02:01] 31 14654 1.5 1 6869 7785 | |
| [2014-10-06 02:01] 32 14319 1.5 1 6364 7955 | |
| [2014-10-06 02:01] 33 13308 1.5 1 5425 7883 | |
| [2014-10-06 02:01] 34 12476 1.5 1 4821 7655 | |
| [2014-10-06 02:01] 35 11550 1.5 1 4322 7228 | |
| [2014-10-06 02:01] 36 11459 1.5 1 4209 7250 | |
| [2014-10-06 02:01] 37 11504 1.5 1 3925 7579 | |
| [2014-10-06 02:01] 38 12134 1.5 1 3892 8242 | |
| [2014-10-06 02:01] 39 11868 1.5 1 3937 7931 | |
| [2014-10-06 02:01] 40 11999 1.5 1 3769 8230 | |
| [2014-10-06 02:01] 41 11084 1.5 1 3640 7444 | |
| [2014-10-06 02:01] 42 11867 1.5 1 3707 8160 | |
| [2014-10-06 02:01] 43 11745 1.5 1 3517 8228 | |
| [2014-10-06 02:01] 44 11572 1.5 1 3499 8073 | |
| [2014-10-06 02:01] 45 10942 1.5 1 3512 7430 | |
| [2014-10-06 02:01] 46 11005 1.5 1 3420 7585 | |
| [2014-10-06 02:01] 47 10875 1.5 1 3184 7691 | |
| [2014-10-06 02:01] 48 10780 1.5 1 3032 7748 | |
| [2014-10-06 02:01] 49 10439 1.5 1 2979 7460 | |
| [2014-10-06 02:01] 50 10192 1.5 1 2777 7415 | |
| [2014-10-06 02:01] 51 9444 1.5 1 2534 6910 | |
| [2014-10-06 02:01] 52 9351 1.5 1 2503 6848 | |
| [2014-10-06 02:01] 53 9211 1.5 1 2423 6788 | |
| [2014-10-06 02:01] 54 9812 1.5 1 2503 7309 | |
| [2014-10-06 02:01] 55 9707 1.5 1 2546 7161 | |
| [2014-10-06 02:01] 56 9651 1.5 1 2277 7374 | |
| [2014-10-06 02:01] 57 9493 1.5 1 2140 7353 | |
| [2014-10-06 02:01] 58 9296 1.5 1 2145 7151 | |
| [2014-10-06 02:01] 59 9172 1.5 1 1981 7191 | |
| [2014-10-06 02:01] 60 9118 1.5 1 2030 7088 | |
| [2014-10-06 02:01] 61 10031 1.5 1 2124 7907 | |
| [2014-10-06 02:01] 62 8766 1.5 1 2006 6760 | |
| [2014-10-06 02:01] 63 8979 1.5 1 1972 7007 | |
| [2014-10-06 02:01] 64 9823 1.5 1 1969 7854 | |
| [2014-10-06 02:01] 65 9420 1.5 1 1961 7459 | |
| [2014-10-06 02:01] 66 9874 1.5 1 2036 7838 | |
| [2014-10-06 02:01] 67 9306 1.5 1 1995 7311 | |
| [2014-10-06 02:01] 68 12227 1.5 1 1857 10370 | |
| [2014-10-06 02:01] 69 11263 1.5 1 1858 9405 | |
| [2014-10-06 02:01] 70 9372 1.5 1 1797 7575 | |
| [2014-10-06 02:01] 71 9719 1.5 1 1844 7875 | |
| [2014-10-06 02:01] 72 9123 1.5 1 1837 7286 | |
| [2014-10-06 02:01] 73 9181 1.5 1 1847 7334 | |
| [2014-10-06 02:01] 74 8855 1.5 1 1787 7068 | |
| [2014-10-06 02:01] 75 8182 1.5 1 1625 6557 | |
| [2014-10-06 02:01] 76 8893 1.5 1 1546 7347 | |
| [2014-10-06 02:01] 77 9209 1.5 1 1733 7476 | |
| [2014-10-06 02:01] 78 11726 1.5 1 1877 9849 | |
| [2014-10-06 02:01] 79 8817 1.5 1 2076 6741 | |
| [2014-10-06 02:01] 80 8858 1.5 1 1713 7145 | |
| [2014-10-06 02:01] 81 8574 1.5 1 1581 6993 | |
| [2014-10-06 02:01] 82 9285 1.5 1 1543 7742 | |
| [2014-10-06 02:01] 83 8600 1.5 1 1540 7060 | |
| [2014-10-06 02:01] 84 10843 1.5 1 1587 9256 | |
| [2014-10-06 02:01] 85 8144 1.5 1 1490 6654 | |
| [2014-10-06 02:01] 86 8004 1.5 1 1480 6524 | |
| [2014-10-06 02:01] 87 7821 1.5 1 1358 6463 | |
| [2014-10-06 02:01] 88 7912 1.5 1 1429 6483 | |
| [2014-10-06 02:01] 89 8776 1.5 1 1464 7312 | |
| [2014-10-06 02:01] 90 10575 1.5 1 1590 8985 | |
| [2014-10-06 02:01] 91 10085 1.5 1 1393 8692 | |
| [2014-10-06 02:01] 92 9056 1.5 1 1335 7721 | |
| [2014-10-06 02:01] 93 7880 1.5 1 1312 6568 | |
| [2014-10-06 02:01] 94 5305 1.5 1 1165 4140 | |
| [2014-10-06 02:01] 95 7216 1.5 1 1227 5989 | |
| [2014-10-06 02:01] 96 6943 1.5 1 1002 5941 | |
| [2014-10-06 02:01] 97 6439 1.5 1 938 5501 | |
| [2014-10-06 02:01] 98 4479 1.5 1 749 3730 | |
| [2014-10-06 02:01] 99 4682 1.5 1 790 3892 | |
| [2014-10-06 02:01] 100 16046 1.5 1 1584 14462 | |
| [2014-10-06 02:01] 101 19936 1.5 1 3176 16760 | |
| [2014-10-06 02:01] | |
| [2014-10-06 02:01] === Adapter 3 === | |
| [2014-10-06 02:01] | |
| [2014-10-06 02:01] Adapter 'AGATCGGAAGAG', length 12, was trimmed 7817560 times. | |
| [2014-10-06 02:01] | |
| [2014-10-06 02:01] No. of allowed errors: | |
| [2014-10-06 02:01] 0-9 bp: 0; 10-12 bp: 1 | |
| [2014-10-06 02:01] | |
| [2014-10-06 02:01] Overview of removed sequences | |
| [2014-10-06 02:01] length count expect max.err error counts | |
| [2014-10-06 02:01] 3 4113504 1618183.0 0 4113504 | |
| [2014-10-06 02:01] 4 1048675 404545.7 0 1048675 | |
| [2014-10-06 02:01] 5 387643 101136.4 0 387643 | |
| [2014-10-06 02:01] 6 272721 25284.1 0 272721 | |
| [2014-10-06 02:01] 7 209446 6321.0 0 209446 | |
| [2014-10-06 02:01] 8 205926 1580.3 0 205926 | |
| [2014-10-06 02:01] 9 171999 395.1 0 168270 3729 | |
| [2014-10-06 02:01] 10 150875 98.8 1 144107 6768 | |
| [2014-10-06 02:01] 11 110019 24.7 1 105512 4507 | |
| [2014-10-06 02:01] 12 107822 6.2 1 105021 2801 | |
| [2014-10-06 02:01] 13 88622 6.2 1 86074 2548 | |
| Traceback (most recent call last): | |
| File "/usr/local/bin/bcbio_nextgen.py", line 216, in <module> | |
| main(**kwargs) | |
| File "/usr/local/bin/bcbio_nextgen.py", line 42, in main | |
| run_main(**kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 36, in run_main | |
| fc_dir, run_info_yaml) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 82, in _run_toplevel | |
| for xs in pipeline.run(config, config_file, parallel, dirs, pipeline_items): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 306, in run | |
| samples = run_parallel("process_alignment", samples) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel | |
| return run_multicore(fn, items, config, parallel=parallel) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 84, in run_multicore | |
| for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 653, in __call__ | |
| self.dispatch(function, args, kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 400, in dispatch | |
| job = ImmediateApply(func, args, kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 138, in __init__ | |
| self.results = func(*args, **kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 63, in wrapper | |
| return apply(f, *args, **kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 27, in process_alignment | |
| return sample.process_alignment(*args) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.py", line 104, in process_alignment | |
| data = align_to_sort_bam(fastq1, fastq2, aligner, data) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.py", line 64, in align_to_sort_bam | |
| names, align_dir, data) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.py", line 98, in _align_from_fastq | |
| out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/tophat.py", line 260, in align | |
| align_dir, data, names) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/tophat.py", line 115, in tophat_align | |
| if _ref_version(ref_file) == 1 or options.get("fusion-search", False): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/tophat.py", line 370, in _ref_version | |
| "(bowtie2)." % (ref_file)) | |
| ValueError: Cannot detect which reference version is. Should end in either .ebwt (bowtie) or .bt2 (bowtie2). | |
| ^C | |
| Killed | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ ls | |
| align checkpoints_parallel log profile provenance trimmed tx | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ pwd | |
| /vagrant_data/seqc-test/seqc/work | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ bcbio_nextgen.py ../config/seqc.yaml -n 8 | |
| [2014-10-07 16:11] Using input YAML configuration: /vagrant_data/seqc-test/seqc/config/seqc.yaml | |
| [2014-10-07 16:11] Checking sample YAML configuration: /vagrant_data/seqc-test/seqc/config/seqc.yaml | |
| [2014-10-07 16:11] Testing minimum versions of installed programs | |
| [2014-10-07 16:11] Resource requests: AlienTrimmer, picard; memory: 2.0, 3.5; cores: 1, 1 | |
| [2014-10-07 16:11] Configuring 4 jobs to run, using 1 cores each with 3.8g of memory reserved for each job | |
| [2014-10-07 16:11] run local -- checkpoint passed: trimming | |
| [2014-10-07 16:11] Timing: adapter trimming | |
| [2014-10-07 16:11] multiprocessing: prepare_sample | |
| [2014-10-07 16:11] Preparing UHRR_rep1 | |
| [2014-10-07 16:11] Preparing HBRR_rep1 | |
| [2014-10-07 16:11] Preparing UHRR_rep2 | |
| [2014-10-07 16:11] Preparing HBRR_rep2 | |
| [2014-10-07 16:11] Preparing UHRR_rep3 | |
| [2014-10-07 16:11] Preparing HBRR_rep3 | |
| [2014-10-07 16:11] multiprocessing: trim_sample | |
| [2014-10-07 16:11] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950078_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950078_2.fastq.gz. | |
| [2014-10-07 16:11] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950079_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950079_2.fastq.gz. | |
| [2014-10-07 16:11] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950080_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950080_2.fastq.gz. | |
| [2014-10-07 16:11] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950081_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950081_2.fastq.gz. | |
| [2014-10-07 16:11] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950082_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950082_2.fastq.gz. | |
| [2014-10-07 16:11] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950083_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950083_2.fastq.gz. | |
| [2014-10-07 16:11] Resource requests: picard, tophat2; memory: 0.4; cores: 1, 16 | |
| [2014-10-07 16:11] Configuring 1 jobs to run, using 8 cores each with 8.2g of memory reserved for each job | |
| [2014-10-07 16:11] Timing: alignment | |
| [2014-10-07 16:11] multiprocessing: process_alignment | |
| [2014-10-07 16:11] Aligning lane 1_2014-10-05_seqc with tophat2 aligner | |
| Traceback (most recent call last): | |
| File "/usr/local/bin/bcbio_nextgen.py", line 216, in <module> | |
| main(**kwargs) | |
| File "/usr/local/bin/bcbio_nextgen.py", line 42, in main | |
| run_main(**kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 36, in run_main | |
| fc_dir, run_info_yaml) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 82, in _run_toplevel | |
| for xs in pipeline.run(config, config_file, parallel, dirs, pipeline_items): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 306, in run | |
| samples = run_parallel("process_alignment", samples) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel | |
| return run_multicore(fn, items, config, parallel=parallel) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 84, in run_multicore | |
| for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 653, in __call__ | |
| self.dispatch(function, args, kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 400, in dispatch | |
| job = ImmediateApply(func, args, kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 138, in __init__ | |
| self.results = func(*args, **kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 63, in wrapper | |
| return apply(f, *args, **kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 27, in process_alignment | |
| return sample.process_alignment(*args) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.py", line 104, in process_alignment | |
| data = align_to_sort_bam(fastq1, fastq2, aligner, data) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.py", line 64, in align_to_sort_bam | |
| names, align_dir, data) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.py", line 98, in _align_from_fastq | |
| out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/tophat.py", line 260, in align | |
| align_dir, data, names) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/tophat.py", line 115, in tophat_align | |
| if _ref_version(ref_file) == 1 or options.get("fusion-search", False): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/tophat.py", line 370, in _ref_version | |
| "(bowtie2)." % (ref_file)) | |
| ValueError: Cannot detect which reference version is. Should end in either .ebwt (bowtie) or .bt2 (bowtie2). | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ ls | |
| align checkpoints_parallel log profile provenance trimmed tx | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ cd checkpoints_parallel/ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work/checkpoints_parallel$ ls | |
| trimming.done | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work/checkpoints_parallel$ rm trimming.done | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work/checkpoints_parallel$ cd .. | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ bcbio_nextgen.py ../config/seqc.yaml -n 8 | |
| [2014-10-07 16:11] Using input YAML configuration: /vagrant_data/seqc-test/seqc/config/seqc.yaml | |
| [2014-10-07 16:11] Checking sample YAML configuration: /vagrant_data/seqc-test/seqc/config/seqc.yaml | |
| [2014-10-07 16:11] Testing minimum versions of installed programs | |
| [2014-10-07 16:11] Resource requests: AlienTrimmer, picard; memory: 2.0, 3.5; cores: 1, 1 | |
| [2014-10-07 16:11] Configuring 4 jobs to run, using 1 cores each with 3.8g of memory reserved for each job | |
| [2014-10-07 16:11] Timing: adapter trimming | |
| [2014-10-07 16:11] multiprocessing: prepare_sample | |
| [2014-10-07 16:11] Preparing UHRR_rep1 | |
| [2014-10-07 16:11] Preparing HBRR_rep1 | |
| ^C[2014-10-07 16:11] Preparing UHRR_rep2 | |
| Process PoolWorker-4: | |
| Traceback (most recent call last): | |
| Process PoolWorker-1: | |
| Traceback (most recent call last): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap | |
| Process PoolWorker-2: | |
| Traceback (most recent call last): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap | |
| self.run() | |
| self.run() | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/multiprocessing/process.py", line 114, in run | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/multiprocessing/process.py", line 114, in run | |
| self._target(*self._args, **self._kwargs) | |
| self.run() | |
| self._target(*self._args, **self._kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/multiprocessing/pool.py", line 102, in worker | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/multiprocessing/pool.py", line 102, in worker | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/multiprocessing/process.py", line 114, in run | |
| self._target(*self._args, **self._kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/multiprocessing/pool.py", line 102, in worker | |
| task = get() | |
| task = get() | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/pool.py", line 343, in get | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/pool.py", line 341, in get | |
| task = get() | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/pool.py", line 341, in get | |
| return recv() | |
| KeyboardInterrupt | |
| racquire() | |
| racquire() | |
| KeyboardInterrupt | |
| KeyboardInterrupt | |
| ls | |
| ^CProcess PoolWorker-3: | |
| Traceback (most recent call last): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap | |
| self.run() | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/multiprocessing/process.py", line 114, in run | |
| self._target(*self._args, **self._kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/multiprocessing/pool.py", line 102, in worker | |
| task = get() | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/pool.py", line 341, in get | |
| racquire() | |
| KeyboardInterrupt | |
| Traceback (most recent call last): | |
| File "/usr/local/bin/bcbio_nextgen.py", line 216, in <module> | |
| main(**kwargs) | |
| File "/usr/local/bin/bcbio_nextgen.py", line 42, in main | |
| run_main(**kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 36, in run_main | |
| fc_dir, run_info_yaml) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 82, in _run_toplevel | |
| for xs in pipeline.run(config, config_file, parallel, dirs, pipeline_items): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 298, in run | |
| samples = run_parallel("prepare_sample", samples) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel | |
| return run_multicore(fn, items, config, parallel=parallel) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 84, in run_multicore | |
| for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 660, in __call__ | |
| self.retrieve() | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 523, in retrieve | |
| self._pool.terminate() | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/pool.py", line 566, in terminate | |
| super(MemmapingPool, self).terminate() | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/multiprocessing/pool.py", line 456, in terminate | |
| self._terminate() | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/multiprocessing/util.py", line 207, in __call__ | |
| res = self._callback(*self._args, **self._kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/multiprocessing/pool.py", line 486, in _terminate_pool | |
| cls._help_stuff_finish(inqueue, task_handler, len(pool)) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/multiprocessing/pool.py", line 471, in _help_stuff_finish | |
| inqueue._rlock.acquire() | |
| KeyboardInterrupt | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ ^C | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ ls | |
| align checkpoints_parallel log profile provenance trimmed tx | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ ls checkpoints_parallel/ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ ls log/ | |
| bcbio-nextgen-commands.log bcbio-nextgen-debug.log bcbio-nextgen.log | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ ls trimmed/ | |
| SRR950078_1.trimmed.fastq.gz SRR950079_2.trimmed.fastq.gz SRR950081_1.trimmed.fastq.gz SRR950082_2.trimmed.fastq.gz tx | |
| SRR950078_2.trimmed.fastq.gz SRR950080_1.trimmed.fastq.gz SRR950081_2.trimmed.fastq.gz SRR950083_1.trimmed.fastq.gz | |
| SRR950079_1.trimmed.fastq.gz SRR950080_2.trimmed.fastq.gz SRR950082_1.trimmed.fastq.gz SRR950083_2.trimmed.fastq.gz | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ cd trimmed/ | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work/trimmed$ rm *.gz | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work/trimmed$ ls tx/ | |
| tmp_NddEp tmpvE9BSV | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work/trimmed$ ls | |
| tx | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work/trimmed$ cd .. | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ ls | |
| align checkpoints_parallel log profile provenance trimmed tx | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ ls align/ | |
| UHRR_rep1 | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ clear | |
| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ bcbio_nextgen.py ../config/seqc.yaml -n 8 | |
| [2014-10-07 16:12] Using input YAML configuration: /vagrant_data/seqc-test/seqc/config/seqc.yaml | |
| [2014-10-07 16:12] Checking sample YAML configuration: /vagrant_data/seqc-test/seqc/config/seqc.yaml | |
| [2014-10-07 16:12] Testing minimum versions of installed programs | |
| [2014-10-07 16:12] Resource requests: AlienTrimmer, picard; memory: 2.0, 3.5; cores: 1, 1 | |
| [2014-10-07 16:12] Configuring 4 jobs to run, using 1 cores each with 3.8g of memory reserved for each job | |
| [2014-10-07 16:12] Timing: adapter trimming | |
| [2014-10-07 16:12] multiprocessing: prepare_sample | |
| [2014-10-07 16:12] Preparing UHRR_rep1 | |
| [2014-10-07 16:12] Preparing HBRR_rep1 | |
| [2014-10-07 16:12] Preparing UHRR_rep2 | |
| [2014-10-07 16:12] Preparing HBRR_rep2 | |
| [2014-10-07 16:12] Preparing UHRR_rep3 | |
| [2014-10-07 16:12] Preparing HBRR_rep3 | |
| [2014-10-07 16:12] multiprocessing: trim_sample | |
| [2014-10-07 16:12] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950078_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950078_2.fastq.gz. | |
| [2014-10-07 16:12] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950079_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950079_2.fastq.gz. | |
| [2014-10-07 16:12] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950080_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950080_2.fastq.gz. | |
| [2014-10-07 16:12] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950081_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950081_2.fastq.gz. | |
| [2014-10-07 16:12] Trimming /vagrant_data/seqc-test/input/SRR950078_1.fastq.gz and /vagrant_data/seqc-test/input/SRR950078_2.fastq.gz in single end mode with cutadapt. | |
| [2014-10-07 16:12] Trimming /vagrant_data/seqc-test/input/SRR950080_1.fastq.gz and /vagrant_data/seqc-test/input/SRR950080_2.fastq.gz in single end mode with cutadapt. | |
| [2014-10-07 16:12] Trimming /vagrant_data/seqc-test/input/SRR950079_1.fastq.gz and /vagrant_data/seqc-test/input/SRR950079_2.fastq.gz in single end mode with cutadapt. | |
| [2014-10-07 16:12] Trimming /vagrant_data/seqc-test/input/SRR950081_1.fastq.gz and /vagrant_data/seqc-test/input/SRR950081_2.fastq.gz in single end mode with cutadapt. | |
| [2014-10-07 18:25] cutadapt version 1.4.2 | |
| [2014-10-07 18:25] Command line parameters: --times=2 --quality-base=33 --quality-cutoff=5 --format=fastq --adapter=AAAAAAAAAAAAA --adapter=TTTTTTTTTTTTT --adapter=AGATCGGAAGAG --adapter=CTCTTCCGATCT --minimum-length=25 -o /vagrant_data/seqc-test/seqc/work/trimmed/SRR950080_1.trimmed.tmp.fastq.gz -p /vagrant_data/seqc-test/seqc/work/trimmed/SRR950080_2.trimmed.tmp.fastq.gz /vagrant_data/seqc-test/input/SRR950080_1.fastq.gz /vagrant_data/seqc-test/input/SRR950080_2.fastq.gz | |
| [2014-10-07 18:25] Maximum error rate: 10.00% | |
| [2014-10-07 18:25] No. of adapters: 4 | |
| [2014-10-07 18:25] Processed reads: 91781477 | |
| [2014-10-07 18:25] Processed bases: 9269929177 bp (9269.9 Mbp) | |
| [2014-10-07 18:25] Trimmed reads: 13369720 (14.6%) | |
| [2014-10-07 18:25] Quality-trimmed: 961422800 bp (961.4 Mbp) (10.37% of total) | |
| [2014-10-07 18:25] Trimmed bases: 398227689 bp (398.2 Mbp) (4.30% of total) | |
| [2014-10-07 18:25] Too short reads: 7258963 (7.9% of processed reads) | |
| [2014-10-07 18:25] Too long reads: 0 (0.0% of processed reads) | |
| [2014-10-07 18:25] Total time: 5517.98 s | |
| [2014-10-07 18:25] Time per read: 0.060 ms | |
| [2014-10-07 18:25] | |
| [2014-10-07 18:25] === Adapter 1 === | |
| [2014-10-07 18:25] | |
| [2014-10-07 18:25] Adapter 'AAAAAAAAAAAAA', length 13, was trimmed 6138253 times. | |
| [2014-10-07 18:25] | |
| [2014-10-07 18:25] No. of allowed errors: | |
| [2014-10-07 18:25] 0-9 bp: 0; 10-13 bp: 1 | |
| [2014-10-07 18:25] | |
| [2014-10-07 18:25] Overview of removed sequences | |
| [2014-10-07 18:25] length count expect max.err error counts | |
| [2014-10-07 18:25] 3 3078661 1434085.6 0 3078661 | |
| [2014-10-07 18:25] 4 1096883 358521.4 0 1096883 | |
| [2014-10-07 18:25] 5 443404 89630.3 0 443404 | |
| [2014-10-07 18:25] 6 153688 22407.6 0 153688 | |
| [2014-10-07 18:25] 7 78772 5601.9 0 78772 | |
| [2014-10-07 18:25] 8 44888 1400.5 0 44888 | |
| [2014-10-07 18:25] 9 36923 350.1 0 36923 | |
| [2014-10-07 18:25] 10 85323 87.5 1 30531 54792 | |
| [2014-10-07 18:25] 11 63040 21.9 1 27611 35429 | |
| [2014-10-07 18:25] 12 56012 5.5 1 32421 23591 | |
| [2014-10-07 18:25] 13 48131 1.4 1 32278 15853 | |
| [2014-10-07 18:25] 14 47228 1.4 1 34381 12847 | |
| [2014-10-07 18:25] 15 44750 1.4 1 33722 11028 | |
| [2014-10-07 18:25] 16 41075 1.4 1 31244 9831 | |
| [2014-10-07 18:25] 17 36962 1.4 1 28057 8905 | |
| [2014-10-07 18:25] 18 32886 1.4 1 24639 8247 | |
| [2014-10-07 18:25] 19 29458 1.4 1 22266 7192 | |
| [2014-10-07 18:25] 20 26461 1.4 1 19310 7151 | |
| [2014-10-07 18:25] 21 25106 1.4 1 17719 7387 | |
| [2014-10-07 18:25] 22 22948 1.4 1 15881 7067 | |
| [2014-10-07 18:25] 23 21206 1.4 1 14337 6869 | |
| [2014-10-07 18:25] 24 20102 1.4 1 13215 6887 | |
| [2014-10-07 18:25] 25 18159 1.4 1 11543 6616 | |
| [2014-10-07 18:25] 26 17376 1.4 1 10637 6739 | |
| [2014-10-07 18:25] 27 15850 1.4 1 9330 6520 | |
| [2014-10-07 18:25] 28 14835 1.4 1 8385 6450 | |
| [2014-10-07 18:25] 29 13665 1.4 1 7386 6279 | |
| [2014-10-07 18:25] 30 13815 1.4 1 6869 6946 | |
| [2014-10-07 18:25] 31 12385 1.4 1 6164 6221 | |
| [2014-10-07 18:25] 32 11582 1.4 1 5674 5908 | |
| [2014-10-07 18:25] 33 11948 1.4 1 5819 6129 | |
| [2014-10-07 18:25] 34 11552 1.4 1 5743 5809 | |
| [2014-10-07 18:25] 35 11027 1.4 1 5475 5552 | |
| [2014-10-07 18:25] 36 10525 1.4 1 4813 5712 | |
| [2014-10-07 18:25] 37 10243 1.4 1 4547 5696 | |
| [2014-10-07 18:25] 38 10625 1.4 1 4326 6299 | |
| [2014-10-07 18:25] 39 9466 1.4 1 3831 5635 | |
| [2014-10-07 18:25] 40 10013 1.4 1 4648 5365 | |
| [2014-10-07 18:25] 41 8999 1.4 1 3888 5111 | |
| [2014-10-07 18:25] 42 9178 1.4 1 4023 5155 | |
| [2014-10-07 18:25] 43 9575 1.4 1 4327 5248 | |
| [2014-10-07 18:25] 44 9751 1.4 1 4236 5515 | |
| [2014-10-07 18:25] 45 8960 1.4 1 3852 5108 | |
| [2014-10-07 18:25] 46 8448 1.4 1 3094 5354 | |
| [2014-10-07 18:25] 47 7739 1.4 1 2687 5052 | |
| [2014-10-07 18:25] 48 8316 1.4 1 2609 5707 | |
| [2014-10-07 18:25] 49 7258 1.4 1 2245 5013 | |
| [2014-10-07 18:25] 50 6948 1.4 1 2000 4948 | |
| [2014-10-07 18:25] 51 6773 1.4 1 2055 4718 | |
| [2014-10-07 18:25] 52 6908 1.4 1 2109 4799 | |
| [2014-10-07 18:25] 53 7097 1.4 1 1970 5127 | |
| [2014-10-07 18:25] 54 7175 1.4 1 2126 5049 | |
| [2014-10-07 18:25] 55 6970 1.4 1 2037 4933 | |
| [2014-10-07 18:25] 56 6865 1.4 1 1987 4878 | |
| [2014-10-07 18:25] 57 7404 1.4 1 1827 5577 | |
| [2014-10-07 18:25] 58 7201 1.4 1 1784 5417 | |
| [2014-10-07 18:25] 59 7058 1.4 1 1931 5127 | |
| [2014-10-07 18:25] 60 6489 1.4 1 1755 4734 | |
| [2014-10-07 18:25] 61 6914 1.4 1 1775 5139 | |
| [2014-10-07 18:25] 62 6993 1.4 1 1981 5012 | |
| [2014-10-07 18:25] 63 6811 1.4 1 1821 4990 | |
| [2014-10-07 18:25] 64 6562 1.4 1 1773 4789 | |
| [2014-10-07 18:25] 65 6467 1.4 1 1630 4837 | |
| [2014-10-07 18:25] 66 6646 1.4 1 1710 4936 | |
| [2014-10-07 18:25] 67 6347 1.4 1 1696 4651 | |
| [2014-10-07 18:25] 68 6625 1.4 1 1740 4885 | |
| [2014-10-07 18:25] 69 6630 1.4 1 1567 5063 | |
| [2014-10-07 18:25] 70 6482 1.4 1 1451 5031 | |
| [2014-10-07 18:25] 71 6504 1.4 1 1526 4978 | |
| [2014-10-07 18:25] 72 6513 1.4 1 1419 5094 | |
| [2014-10-07 18:25] 73 6610 1.4 1 1485 5125 | |
| [2014-10-07 18:25] 74 6627 1.4 1 1400 5227 | |
| [2014-10-07 18:25] 75 6259 1.4 1 1386 4873 | |
| [2014-10-07 18:25] 76 6616 1.4 1 1327 5289 | |
| [2014-10-07 18:25] 77 5875 1.4 1 1122 4753 | |
| [2014-10-07 18:25] 78 6377 1.4 1 1330 5047 | |
| [2014-10-07 18:25] 79 6189 1.4 1 1350 4839 | |
| [2014-10-07 18:25] 80 6315 1.4 1 1264 5051 | |
| [2014-10-07 18:25] 81 5657 1.4 1 1135 4522 | |
| [2014-10-07 18:25] 82 6107 1.4 1 1241 4866 | |
| [2014-10-07 18:25] 83 5900 1.4 1 1197 4703 | |
| [2014-10-07 18:25] 84 5735 1.4 1 1322 4413 | |
| [2014-10-07 18:25] 85 5831 1.4 1 1308 4523 | |
| [2014-10-07 18:25] 86 6087 1.4 1 1421 4666 | |
| [2014-10-07 18:25] 87 5966 1.4 1 1261 4705 | |
| [2014-10-07 18:25] 88 5437 1.4 1 1115 4322 | |
| [2014-10-07 18:25] 89 5627 1.4 1 937 4690 | |
| [2014-10-07 18:25] 90 4727 1.4 1 809 3918 | |
| [2014-10-07 18:25] 91 3731 1.4 1 678 3053 | |
| [2014-10-07 18:25] 92 6560 1.4 1 1151 5409 | |
| [2014-10-07 18:25] 93 7240 1.4 1 1192 6048 | |
| [2014-10-07 18:25] 94 6297 1.4 1 904 5393 | |
| [2014-10-07 18:25] 95 3461 1.4 1 547 2914 | |
| [2014-10-07 18:25] 96 2783 1.4 1 550 2233 | |
| [2014-10-07 18:25] 97 3436 1.4 1 540 2896 | |
| [2014-10-07 18:25] 98 3964 1.4 1 516 3448 | |
| [2014-10-07 18:25] 99 3122 1.4 1 394 2728 | |
| [2014-10-07 18:25] 100 6380 1.4 1 662 5718 | |
| [2014-10-07 18:25] 101 11758 1.4 1 1148 10610 | |
| [2014-10-07 18:25] | |
| [2014-10-07 18:25] === Adapter 2 === | |
| [2014-10-07 18:25] | |
| [2014-10-07 18:25] Adapter 'TTTTTTTTTTTTT', length 13, was trimmed 6142076 times. | |
| [2014-10-07 18:25] | |
| [2014-10-07 18:25] No. of allowed errors: | |
| [2014-10-07 18:25] 0-9 bp: 0; 10-13 bp: 1 | |
| [2014-10-07 18:25] | |
| [2014-10-07 18:25] Overview of removed sequences | |
| [2014-10-07 18:25] length count expect max.err error counts | |
| [2014-10-07 18:25] 3 3046218 1434085.6 0 3046218 | |
| [2014-10-07 18:25] 4 1082057 358521.4 0 1082057 | |
| [2014-10-07 18:25] 5 410270 89630.3 0 410270 | |
| [2014-10-07 18:25] 6 139456 22407.6 0 139456 | |
| [2014-10-07 18:25] 7 77384 5601.9 0 77384 | |
| [2014-10-07 18:25] 8 31583 1400.5 0 31583 | |
| [2014-10-07 18:25] 9 24796 350.1 0 24796 | |
| [2014-10-07 18:25] 10 78082 87.5 1 21661 56421 | |
| [2014-10-07 18:25] 11 58493 21.9 1 20535 37958 | |
| [2014-10-07 18:25] 12 61226 5.5 1 35979 25247 | |
| [2014-10-07 18:25] 13 57811 1.4 1 40029 17782 | |
| [2014-10-07 18:25] 14 62430 1.4 1 47877 14553 | |
| [2014-10-07 18:25] 15 64933 1.4 1 52535 12398 | |
| [2014-10-07 18:25] 16 61640 1.4 1 51111 10529 | |
| [2014-10-07 18:25] 17 56259 1.4 1 46413 9846 | |
| [2014-10-07 18:25] 18 46388 1.4 1 37307 9081 | |
| [2014-10-07 18:25] 19 39173 1.4 1 30120 9053 | |
| [2014-10-07 18:25] 20 41023 1.4 1 26733 14290 | |
| [2014-10-07 18:25] 21 32259 1.4 1 23838 8421 | |
| [2014-10-07 18:25] 22 28038 1.4 1 20159 7879 | |
| [2014-10-07 18:25] 23 25344 1.4 1 17626 7718 | |
| [2014-10-07 18:25] 24 23776 1.4 1 14973 8803 | |
| [2014-10-07 18:25] 25 21143 1.4 1 12659 8484 | |
| [2014-10-07 18:25] 26 18010 1.4 1 10967 7043 | |
| [2014-10-07 18:25] 27 16619 1.4 1 9534 7085 | |
| [2014-10-07 18:25] 28 15546 1.4 1 8186 7360 | |
| [2014-10-07 18:25] 29 14522 1.4 1 7193 7329 | |
| [2014-10-07 18:25] 30 13153 1.4 1 6231 6922 | |
| [2014-10-07 18:25] 31 12151 1.4 1 5528 6623 | |
| [2014-10-07 18:25] 32 11793 1.4 1 4928 6865 | |
| [2014-10-07 18:25] 33 10759 1.4 1 4371 6388 | |
| [2014-10-07 18:25] 34 10052 1.4 1 3773 6279 | |
| [2014-10-07 18:25] 35 9270 1.4 1 3173 6097 | |
| [2014-10-07 18:25] 36 9155 1.4 1 3065 6090 | |
| [2014-10-07 18:25] 37 9452 1.4 1 3259 6193 | |
| [2014-10-07 18:25] 38 9066 1.4 1 2932 6134 | |
| [2014-10-07 18:25] 39 8821 1.4 1 2614 6207 | |
| [2014-10-07 18:25] 40 8914 1.4 1 2787 6127 | |
| [2014-10-07 18:25] 41 8800 1.4 1 2764 6036 | |
| [2014-10-07 18:25] 42 8929 1.4 1 2646 6283 | |
| [2014-10-07 18:25] 43 9440 1.4 1 2826 6614 | |
| [2014-10-07 18:25] 44 8579 1.4 1 2543 6036 | |
| [2014-10-07 18:25] 45 8857 1.4 1 2628 6229 | |
| [2014-10-07 18:25] 46 8155 1.4 1 2371 5784 | |
| [2014-10-07 18:25] 47 8298 1.4 1 2477 5821 | |
| [2014-10-07 18:25] 48 8374 1.4 1 2340 6034 | |
| [2014-10-07 18:25] 49 7881 1.4 1 1959 5922 | |
| [2014-10-07 18:25] 50 7932 1.4 1 1982 5950 | |
| [2014-10-07 18:25] 51 7185 1.4 1 1809 5376 | |
| [2014-10-07 18:25] 52 6770 1.4 1 1646 5124 | |
| [2014-10-07 18:25] 53 6594 1.4 1 1687 4907 | |
| [2014-10-07 18:25] 54 7145 1.4 1 1669 5476 | |
| [2014-10-07 18:25] 55 6865 1.4 1 1758 5107 | |
| [2014-10-07 18:25] 56 6938 1.4 1 1720 5218 | |
| [2014-10-07 18:25] 57 6836 1.4 1 1522 5314 | |
| [2014-10-07 18:25] 58 6406 1.4 1 1444 4962 | |
| [2014-10-07 18:25] 59 7025 1.4 1 1402 5623 | |
| [2014-10-07 18:25] 60 6447 1.4 1 1313 5134 | |
| [2014-10-07 18:25] 61 6623 1.4 1 1356 5267 | |
| [2014-10-07 18:25] 62 6332 1.4 1 1336 4996 | |
| [2014-10-07 18:25] 63 6254 1.4 1 1263 4991 | |
| [2014-10-07 18:25] 64 6307 1.4 1 1294 5013 | |
| [2014-10-07 18:25] 65 6096 1.4 1 1138 4958 | |
| [2014-10-07 18:25] 66 6363 1.4 1 1181 5182 | |
| [2014-10-07 18:25] 67 6304 1.4 1 1239 5065 | |
| [2014-10-07 18:25] 68 6170 1.4 1 1175 4995 | |
| [2014-10-07 18:25] 69 6269 1.4 1 1191 5078 | |
| [2014-10-07 18:25] 70 6220 1.4 1 1150 5070 | |
| [2014-10-07 18:25] 71 6076 1.4 1 1168 4908 | |
| [2014-10-07 18:25] 72 6374 1.4 1 1133 5241 | |
| [2014-10-07 18:25] 73 5867 1.4 1 1166 4701 | |
| [2014-10-07 18:25] 74 5923 1.4 1 1047 4876 | |
| [2014-10-07 18:25] 75 5399 1.4 1 961 4438 | |
| [2014-10-07 18:25] 76 5547 1.4 1 996 4551 | |
| [2014-10-07 18:25] 77 6210 1.4 1 1019 5191 | |
| [2014-10-07 18:25] 78 5453 1.4 1 920 4533 | |
| [2014-10-07 18:25] 79 5526 1.4 1 988 4538 | |
| [2014-10-07 18:25] 80 6170 1.4 1 940 5230 | |
| [2014-10-07 18:25] 81 5936 1.4 1 886 5050 | |
| [2014-10-07 18:25] 82 5786 1.4 1 811 4975 | |
| [2014-10-07 18:25] 83 5223 1.4 1 862 4361 | |
| [2014-10-07 18:25] 84 5546 1.4 1 919 4627 | |
| [2014-10-07 18:25] 85 5285 1.4 1 835 4450 | |
| [2014-10-07 18:25] 86 5388 1.4 1 793 4595 | |
| [2014-10-07 18:25] 87 5089 1.4 1 699 4390 | |
| [2014-10-07 18:25] 88 5277 1.4 1 742 4535 | |
| [2014-10-07 18:25] 89 5318 1.4 1 817 4501 | |
| [2014-10-07 18:25] 90 7358 1.4 1 957 6401 | |
| [2014-10-07 18:25] 91 6137 1.4 1 850 5287 | |
| [2014-10-07 18:25] 92 6029 1.4 1 757 5272 | |
| [2014-10-07 18:25] 93 5240 1.4 1 700 4540 | |
| [2014-10-07 18:25] 94 3630 1.4 1 511 3119 | |
| [2014-10-07 18:25] 95 4844 1.4 1 637 4207 | |
| [2014-10-07 18:25] 96 4325 1.4 1 524 3801 | |
| [2014-10-07 18:25] 97 4551 1.4 1 451 4100 | |
| [2014-10-07 18:25] 98 3182 1.4 1 343 2839 | |
| [2014-10-07 18:25] 99 2614 1.4 1 272 2342 | |
| [2014-10-07 18:25] 100 10772 1.4 1 646 10126 | |
| [2014-10-07 18:25] 101 12542 1.4 1 1506 11036 | |
| [2014-10-07 18:25] | |
| [2014-10-07 18:25] === Adapter 3 === | |
| [2014-10-07 18:25] | |
| [2014-10-07 18:25] Adapter 'AGATCGGAAGAG', length 12, was trimmed 9557079 times. | |
| [2014-10-07 18:25] | |
| [2014-10-07 18:25] No. of allowed errors: | |
| [2014-10-07 18:25] 0-9 bp: 0; 10-12 bp: 1 | |
| [2014-10-07 18:25] | |
| [2014-10-07 18:25] Overview of removed sequences | |
| [2014-10-07 18:25] length count expect max.err error counts | |
| [2014-10-07 18:25] 3 3552515 1434085.6 0 3552515 | |
| [2014-10-07 18:25] 4 894836 358521.4 0 894836 | |
| [2014-10-07 18:25] 5 321835 89630.3 0 321835 | |
| [2014-10-07 18:25] 6 238085 22407.6 0 238085 | |
| [2014-10-07 18:25] 7 160406 5601.9 0 160406 | |
| [2014-10-07 18:25] 8 182795 1400.5 0 182795 | |
| [2014-10-07 18:25] 9 141380 350.1 0 135774 5606 | |
| [2014-10-07 18:25] 10 116138 87.5 1 108024 8114 | |
| [2014-10-07 18:25] 11 90779 21.9 1 84426 6353 | |
| [2014-10-07 18:25] 12 86751 5.5 1 82981 3770 | |
| [2014-10-07 18:25] 13 60175 5.5 1 57041 3134 | |
| [2014-10-07 18:25] 14 59034 5.5 1 56459 2575 | |
| [2014-10-07 18:25] 15 51905 5.5 1 49104 2801 | |
| [2014-10-07 18:25] 16 44800 5.5 1 42046 2754 | |
| [2014-10-07 18:25] 17 45535 5.5 1 42598 2937 | |
| [2014-10-07 18:25] 18 40257 5.5 1 38010 2247 | |
| [2014-10-07 18:25] 19 26159 5.5 1 24165 1994 | |
| [2014-10-07 18:25] 20 26426 5.5 1 23993 2433 | |
| [2014-10-07 18:25] 21 22987 5.5 1 20620 2367 | |
| [2014-10-07 18:25] 22 22097 5.5 1 16753 5344 | |
| [2014-10-07 18:25] 23 17920 5.5 1 15018 2902 | |
| [2014-10-07 18:25] 24 13733 5.5 1 11652 2081 | |
| [2014-10-07 18:25] 25 13929 5.5 1 12062 1867 | |
| [2014-10-07 18:25] 26 12526 5.5 1 9871 2655 | |
| [2014-10-07 18:25] 27 17541 5.5 1 12143 5398 | |
| [2014-10-07 18:25] 28 13281 5.5 1 10070 3211 | |
| [2014-10-07 18:25] 29 12171 5.5 1 8541 3630 | |
| [2014-10-07 18:25] 30 11523 5.5 1 9099 2424 | |
| [2014-10-07 18:25] 31 7881 5.5 1 4731 3150 | |
| [2014-10-07 18:25] 32 8457 5.5 1 4977 3480 | |
| [2014-10-07 18:25] 33 9573 5.5 1 4647 4926 | |
| [2014-10-07 18:25] 34 11000 5.5 1 5605 5395 | |
| [2014-10-07 18:25] 35 13820 5.5 1 4955 8865 | |
| [2014-10-07 18:25] 36 15423 5.5 1 6125 9298 | |
| [2014-10-07 18:25] 37 20144 5.5 1 6283 13861 | |
| [2014-10-07 18:25] 38 15882 5.5 1 10324 5558 | |
| [2014-10-07 18:25] 39 11832 5.5 1 3785 8047 | |
| [2014-10-07 18:25] 40 12187 5.5 1 4346 7841 | |
| [2014-10-07 18:25] 41 9495 5.5 1 5298 4197 | |
| [2014-10-07 18:25] 42 6244 5.5 1 3241 3003 | |
| [2014-10-07 18:25] 43 5109 5.5 1 2412 2697 | |
| [2014-10-07 18:25] 44 6460 5.5 1 1957 4503 | |
| [2014-10-07 18:25] 45 6791 5.5 1 2297 4494 | |
| [2014-10-07 18:25] 46 6005 5.5 1 2855 3150 | |
| [2014-10-07 18:25] 47 5390 5.5 1 1768 3622 | |
| [2014-10-07 18:25] 48 6705 5.5 1 2318 4387 | |
| [2014-10-07 18:25] 49 6065 5.5 1 2415 3650 | |
| [2014-10-07 18:25] 50 8726 5.5 1 1931 6795 | |
| [2014-10-07 18:25] 51 10147 5.5 1 2673 7474 | |
| [2014-10-07 18:25] 52 12419 5.5 1 3225 9194 | |
| [2014-10-07 18:25] 53 6717 5.5 1 3371 3346 | |
| [2014-10-07 18:25] 54 5085 5.5 1 1476 3609 | |
| [2014-10-07 18:25] 55 7308 5.5 1 1441 5867 | |
| [2014-10-07 18:25] 56 9401 5.5 1 2514 6887 | |
| [2014-10-07 18:25] 57 11073 5.5 1 2205 8868 | |
| [2014-10-07 18:25] 58 14566 5.5 1 2974 11592 | |
| [2014-10-07 18:25] 59 12731 5.5 1 3503 9228 | |
| [2014-10-07 18:25] 60 16189 5.5 1 2782 13407 | |
| [2014-10-07 18:25] 61 22181 5.5 1 3215 18966 | |
| [2014-10-07 18:25] 62 53224 5.5 1 5544 47680 | |
| [2014-10-07 18:25] 63 87515 5.5 1 9321 78194 | |
| [2014-10-07 18:25] 64 54176 5.5 1 14665 39511 | |
| [2014-10-07 18:25] 65 48952 5.5 1 7497 41455 | |
| [2014-10-07 18:25] 66 83728 5.5 1 8951 74777 | |
| [2014-10-07 18:25] 67 140837 5.5 1 14621 126216 | |
| [2014-10-07 18:25] 68 265393 5.5 1 24818 240575 | |
| [2014-10-07 18:25] 69 486514 5.5 1 45481 44103 |
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