Created
July 27, 2016 15:40
-
-
Save ohofmann/ff71a149022372fd30fe7c07157b3cc4 to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 2016-07-27 23:57:53.400 [IPEngineApp] Using existing profile dir: u'/scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/log/ipython' | |
| 2016-07-27 23:57:53.419 [IPEngineApp] Loading url_file u'/scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/log/ipython/security/ipcontroller-1c9737c4-68fd-49be-b74e-85d8bdda4c49-engine.json' | |
| 2016-07-27 23:57:53.461 [IPEngineApp] Registering with controller at tcp://45.113.233.138:59195 | |
| 2016-07-27 23:57:53.623 [IPEngineApp] Starting to monitor the heartbeat signal from the hub every 5010 ms. | |
| 2016-07-27 23:57:53.634 [IPEngineApp] Using existing profile dir: u'/scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/log/ipython' | |
| 2016-07-27 23:57:53.637 [IPEngineApp] Completed registration with id 1 | |
| 2016-07-28 00:14:25.604 [IPEngineApp] WARNING | No heartbeat in the last 5010 ms (1 time(s) in a row). | |
| cat: write error: Broken pipe | |
| cat: write error: Broken pipe | |
| 2016-07-28 00:20:01.180 [IPEngineApp] Exception in apply request: | |
| [0;31m[0m | |
| [0;31mCalledProcessError[0mTraceback (most recent call last) | |
| [0;32m<string>[0m in [0;36m<module>[0;34m()[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc[0m in [0;36m__call__[0;34m(self, *args, **kwargs)[0m | |
| [1;32m 71[0m [0;34m[0m[0m | |
| [1;32m 72[0m [0;32mdef[0m [0m__call__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m---> 73[0;31m [0;32mreturn[0m [0mself[0m[0;34m.[0m[0mf[0m[0;34m([0m[0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 74[0m [0;34m[0m[0m | |
| [1;32m 75[0m [0;32mif[0m [0;32mnot[0m [0mpy3compat[0m[0;34m.[0m[0mPY3[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc[0m in [0;36mprocess_alignment[0;34m(*args)[0m | |
| [1;32m 179[0m [0margs[0m [0;34m=[0m [0mipython[0m[0;34m.[0m[0munzip_args[0m[0;34m([0m[0margs[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 180[0m [0;32mwith[0m [0m_setup_logging[0m[0;34m([0m[0margs[0m[0;34m)[0m [0;32mas[0m [0mconfig[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m--> 181[0;31m [0;32mreturn[0m [0mipython[0m[0;34m.[0m[0mzip_args[0m[0;34m([0m[0mapply[0m[0;34m([0m[0msample[0m[0;34m.[0m[0mprocess_alignment[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 182[0m [0;34m[0m[0m | |
| [1;32m 183[0m [0;34m@[0m[0mrequire[0m[0;34m([0m[0malignprep[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc[0m in [0;36mprocess_alignment[0;34m(data, alt_input)[0m | |
| [1;32m 110[0m [0;32mif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0maligner[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 111[0m [0mlogger[0m[0;34m.[0m[0minfo[0m[0;34m([0m[0;34m"Aligning lane %s with %s aligner"[0m [0;34m%[0m [0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"rgnames"[0m[0;34m][0m[0;34m[[0m[0;34m"lane"[0m[0;34m][0m[0;34m,[0m [0maligner[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m--> 112[0;31m [0mdata[0m [0;34m=[0m [0malign_to_sort_bam[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0maligner[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 113[0m [0mdata[0m [0;34m=[0m [0m_add_supplemental_bams[0m[0;34m([0m[0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 114[0m [0;32melif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0mfastq1[0m[0;34m.[0m[0mendswith[0m[0;34m([0m[0;34m".bam"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36malign_to_sort_bam[0;34m(fastq1, fastq2, aligner, data)[0m | |
| [1;32m 62[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 63[0m data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file, | |
| [0;32m---> 64[0;31m names, align_dir, data) | |
| [0m[1;32m 65[0m [0;32mif[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;32mand[0m [0mutils[0m[0;34m.[0m[0mfile_exists[0m[0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 66[0m [0;32mif[0m [0;32mnot[0m [0mdata[0m[0;34m.[0m[0mget[0m[0;34m([0m[0;34m"align_split"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36m_align_from_fastq[0;34m(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)[0m | |
| [1;32m 115[0m [0mconfig[0m [0;34m=[0m [0mdata[0m[0;34m[[0m[0;34m"config"[0m[0;34m][0m[0;34m[0m[0m | |
| [1;32m 116[0m [0malign_fn[0m [0;34m=[0m [0mTOOLS[0m[0;34m[[0m[0maligner[0m[0;34m][0m[0;34m.[0m[0malign_fn[0m[0;34m[0m[0m | |
| [0;32m--> 117[0;31m [0mout[0m [0;34m=[0m [0malign_fn[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0malign_ref[0m[0;34m,[0m [0mnames[0m[0;34m,[0m [0malign_dir[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 118[0m [0;31m# handle align functions that update the main data dictionary in place[0m[0;34m[0m[0;34m[0m[0m | |
| [1;32m 119[0m [0;32mif[0m [0misinstance[0m[0;34m([0m[0mout[0m[0;34m,[0m [0mdict[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36malign_pipe[0;34m(fastq_file, pair_file, ref_file, names, align_dir, data)[0m | |
| [1;32m 145[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 146[0m out_file = _align_mem(fastq_file, pair_file, ref_file, out_file, | |
| [0;32m--> 147[0;31m names, rg_info, data) | |
| [0m[1;32m 148[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;34m=[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 149[0m [0;32mreturn[0m [0mdata[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36m_align_mem[0;34m(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)[0m | |
| [1;32m 155[0m [0mcmd[0m [0;34m=[0m [0;34m"%s | %s"[0m [0;34m%[0m [0;34m([0m[0m_get_bwa_mem_cmd[0m[0;34m([0m[0mdata[0m[0;34m,[0m [0mout_file[0m[0;34m,[0m [0mref_file[0m[0;34m,[0m [0mfastq_file[0m[0;34m,[0m [0mpair_file[0m[0;34m)[0m[0;34m,[0m [0mtobam_cl[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 156[0m do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None, | |
| [0;32m--> 157[0;31m [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)]) | |
| [0m[1;32m 158[0m [0;32mreturn[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 159[0m [0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36mrun[0;34m(cmd, descr, data, checks, region, log_error, log_stdout)[0m | |
| [1;32m 19[0m [0;32mtry[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 20[0m [0mlogger_cl[0m[0;34m.[0m[0mdebug[0m[0;34m([0m[0;34m" "[0m[0;34m.[0m[0mjoin[0m[0;34m([0m[0mstr[0m[0;34m([0m[0mx[0m[0;34m)[0m [0;32mfor[0m [0mx[0m [0;32min[0m [0mcmd[0m[0;34m)[0m [0;32mif[0m [0;32mnot[0m [0misinstance[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mbasestring[0m[0;34m)[0m [0;32melse[0m [0mcmd[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 21[0;31m [0m_do_run[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mchecks[0m[0;34m,[0m [0mlog_stdout[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 22[0m [0;32mexcept[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 23[0m [0mdiagnostics[0m[0;34m.[0m[0mend_cmd[0m[0;34m([0m[0mcmd_id[0m[0;34m,[0m [0mFalse[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36m_do_run[0;34m(cmd, checks, log_stdout)[0m | |
| [1;32m 93[0m [0ms[0m[0;34m.[0m[0mcommunicate[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 94[0m [0ms[0m[0;34m.[0m[0mstdout[0m[0;34m.[0m[0mclose[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 95[0;31m [0;32mraise[0m [0msubprocess[0m[0;34m.[0m[0mCalledProcessError[0m[0;34m([0m[0mexitcode[0m[0;34m,[0m [0merror_msg[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 96[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 97[0m [0;32mbreak[0m[0;34m[0m[0m | |
| [0;31mCalledProcessError[0m: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-1\tPL:illumina\tPU:NA12878-1\tSM:NA12878-1' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 160000001 176313700) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 160000001 176313700) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/ba32afa0-2972-4129-8d21-48a0979cb4d5/tmpab_qQl/NA12878-1-sort-160000001_176313700-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/bc0bdd5f-dfe7-43b5-9a40-3d1888b0eb2f/tmp8Wb415/NA12878-1-sort-160000001_176313700-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/ba32afa0-2972-4129-8d21-48a0979cb4d5/tmpab_qQl/NA12878-1-sort-160000001_176313700-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/d78e89f5-1a1d-44af-ab5d-47f76ada41a9/tmpYnQyqk/NA12878-1-sort-160000001_176313700-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/ba32afa0-2972-4129-8d21-48a0979cb4d5/tmpab_qQl/NA12878-1-sort-160000001_176313700-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/ba32afa0-2972-4129-8d21-48a0979cb4d5/tmpab_qQl/NA12878-1-sort-160000001_176313700.bam /dev/stdin | |
| [W::sam_hdr_parse] duplicated sequence 'GL000216.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000215.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000205.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000219.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000224.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000223.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000195.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000212.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000222.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000200.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000193.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000194.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000225.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000192.1' | |
| duplicating @RG line NA12878-1 | |
| duplicating @PG line bwa | |
| duplicating @SQ line 1 | |
| duplicating @SQ line 2 | |
| duplicating @SQ line 3 | |
| duplicating @SQ line 4 | |
| duplicating @SQ line 5 | |
| duplicating @SQ line 6 | |
| duplicating @SQ line 7 | |
| duplicating @SQ line 8 | |
| duplicating @SQ line 9 | |
| duplicating @SQ line 10 | |
| duplicating @SQ line 11 | |
| duplicating @SQ line 12 | |
| duplicating @SQ line 13 | |
| duplicating @SQ line 14 | |
| duplicating @SQ line 15 | |
| duplicating @SQ line 16 | |
| duplicating @SQ line 17 | |
| duplicating @SQ line 18 | |
| duplicating @SQ line 19 | |
| duplicating @SQ line 20 | |
| duplicating @SQ line 21 | |
| duplicating @SQ line 22 | |
| duplicating @SQ line X | |
| duplicating @SQ line Y | |
| duplicating @SQ line MT | |
| duplicating @SQ line GL000207.1 | |
| duplicating @SQ line GL000226.1 | |
| duplicating @SQ line GL000229.1 | |
| duplicating @SQ line GL000231.1 | |
| duplicating @SQ line GL000210.1 | |
| duplicating @SQ line GL000239.1 | |
| duplicating @SQ line GL000235.1 | |
| duplicating @SQ line GL000201.1 | |
| duplicating @SQ line GL000247.1 | |
| duplicating @SQ line GL000245.1 | |
| duplicating @SQ line GL000197.1 | |
| duplicating @SQ line GL000203.1 | |
| duplicating @SQ line GL000246.1 | |
| duplicating @SQ line GL000249.1 | |
| duplicating @SQ line GL000196.1 | |
| duplicating @SQ line GL000248.1 | |
| duplicating @SQ line GL000244.1 | |
| duplicating @SQ line GL000238.1 | |
| duplicating @SQ line GL000202.1 | |
| duplicating @SQ line GL000234.1 | |
| duplicating @SQ line GL000232.1 | |
| duplicating @SQ line GL000206.1 | |
| duplicating @SQ line GL000240.1 | |
| duplicating @SQ line GL000236.1 | |
| duplicating @SQ line GL000241.1 | |
| duplicating @SQ line GL000243.1 | |
| duplicating @SQ line GL000242.1 | |
| duplicating @SQ line GL000230.1 | |
| duplicating @SQ line GL000237.1 | |
| duplicating @SQ line GL000233.1 | |
| duplicating @SQ line GL000204.1 | |
| duplicating @SQ line GL000198.1 | |
| duplicating @SQ line GL000208.1 | |
| duplicating @SQ line GL000191.1 | |
| duplicating @SQ line GL000227.1 | |
| duplicating @SQ line GL000228.1 | |
| duplicating @SQ line GL000214.1 | |
| duplicating @SQ line GL000221.1 | |
| duplicating @SQ line GL000209.1 | |
| duplicating @SQ line GL000218.1 | |
| duplicating @SQ line GL000220.1 | |
| duplicating @SQ line GL000213.1 | |
| duplicating @SQ line GL000211.1 | |
| duplicating @SQ line GL000199.1 | |
| duplicating @SQ line GL000217.1 | |
| duplicating @SQ line GL000216.1 | |
| duplicating @SQ line GL000215.1 | |
| duplicating @SQ line GL000205.1 | |
| duplicating @SQ line GL000219.1 | |
| duplicating @SQ line GL000224.1 | |
| duplicating @SQ line GL000223.1 | |
| duplicating @SQ line GL000195.1 | |
| duplicating @SQ line GL000212.1 | |
| duplicating @SQ line GL000222.1 | |
| duplicating @SQ line GL000200.1 | |
| duplicating @SQ line GL000193.1 | |
| duplicating @SQ line GL000194.1 | |
| duplicating @SQ line GL000225.1 | |
| duplicating @SQ line GL000192.1 | |
| ' returned non-zero exit status 1 | |
| cat: write error: Broken pipe | |
| 2016-07-28 00:20:25.145 [IPEngineApp] Exception in apply request: | |
| [0;31m[0m | |
| [0;31mCalledProcessError[0mTraceback (most recent call last) | |
| [0;32m<string>[0m in [0;36m<module>[0;34m()[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc[0m in [0;36m__call__[0;34m(self, *args, **kwargs)[0m | |
| [1;32m 71[0m [0;34m[0m[0m | |
| [1;32m 72[0m [0;32mdef[0m [0m__call__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m---> 73[0;31m [0;32mreturn[0m [0mself[0m[0;34m.[0m[0mf[0m[0;34m([0m[0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 74[0m [0;34m[0m[0m | |
| [1;32m 75[0m [0;32mif[0m [0;32mnot[0m [0mpy3compat[0m[0;34m.[0m[0mPY3[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc[0m in [0;36mprocess_alignment[0;34m(*args)[0m | |
| [1;32m 179[0m [0margs[0m [0;34m=[0m [0mipython[0m[0;34m.[0m[0munzip_args[0m[0;34m([0m[0margs[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 180[0m [0;32mwith[0m [0m_setup_logging[0m[0;34m([0m[0margs[0m[0;34m)[0m [0;32mas[0m [0mconfig[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m--> 181[0;31m [0;32mreturn[0m [0mipython[0m[0;34m.[0m[0mzip_args[0m[0;34m([0m[0mapply[0m[0;34m([0m[0msample[0m[0;34m.[0m[0mprocess_alignment[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 182[0m [0;34m[0m[0m | |
| [1;32m 183[0m [0;34m@[0m[0mrequire[0m[0;34m([0m[0malignprep[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc[0m in [0;36mprocess_alignment[0;34m(data, alt_input)[0m | |
| [1;32m 110[0m [0;32mif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0maligner[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 111[0m [0mlogger[0m[0;34m.[0m[0minfo[0m[0;34m([0m[0;34m"Aligning lane %s with %s aligner"[0m [0;34m%[0m [0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"rgnames"[0m[0;34m][0m[0;34m[[0m[0;34m"lane"[0m[0;34m][0m[0;34m,[0m [0maligner[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m--> 112[0;31m [0mdata[0m [0;34m=[0m [0malign_to_sort_bam[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0maligner[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 113[0m [0mdata[0m [0;34m=[0m [0m_add_supplemental_bams[0m[0;34m([0m[0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 114[0m [0;32melif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0mfastq1[0m[0;34m.[0m[0mendswith[0m[0;34m([0m[0;34m".bam"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36malign_to_sort_bam[0;34m(fastq1, fastq2, aligner, data)[0m | |
| [1;32m 62[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 63[0m data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file, | |
| [0;32m---> 64[0;31m names, align_dir, data) | |
| [0m[1;32m 65[0m [0;32mif[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;32mand[0m [0mutils[0m[0;34m.[0m[0mfile_exists[0m[0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 66[0m [0;32mif[0m [0;32mnot[0m [0mdata[0m[0;34m.[0m[0mget[0m[0;34m([0m[0;34m"align_split"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36m_align_from_fastq[0;34m(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)[0m | |
| [1;32m 115[0m [0mconfig[0m [0;34m=[0m [0mdata[0m[0;34m[[0m[0;34m"config"[0m[0;34m][0m[0;34m[0m[0m | |
| [1;32m 116[0m [0malign_fn[0m [0;34m=[0m [0mTOOLS[0m[0;34m[[0m[0maligner[0m[0;34m][0m[0;34m.[0m[0malign_fn[0m[0;34m[0m[0m | |
| [0;32m--> 117[0;31m [0mout[0m [0;34m=[0m [0malign_fn[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0malign_ref[0m[0;34m,[0m [0mnames[0m[0;34m,[0m [0malign_dir[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 118[0m [0;31m# handle align functions that update the main data dictionary in place[0m[0;34m[0m[0;34m[0m[0m | |
| [1;32m 119[0m [0;32mif[0m [0misinstance[0m[0;34m([0m[0mout[0m[0;34m,[0m [0mdict[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36malign_pipe[0;34m(fastq_file, pair_file, ref_file, names, align_dir, data)[0m | |
| [1;32m 145[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 146[0m out_file = _align_mem(fastq_file, pair_file, ref_file, out_file, | |
| [0;32m--> 147[0;31m names, rg_info, data) | |
| [0m[1;32m 148[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;34m=[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 149[0m [0;32mreturn[0m [0mdata[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36m_align_mem[0;34m(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)[0m | |
| [1;32m 155[0m [0mcmd[0m [0;34m=[0m [0;34m"%s | %s"[0m [0;34m%[0m [0;34m([0m[0m_get_bwa_mem_cmd[0m[0;34m([0m[0mdata[0m[0;34m,[0m [0mout_file[0m[0;34m,[0m [0mref_file[0m[0;34m,[0m [0mfastq_file[0m[0;34m,[0m [0mpair_file[0m[0;34m)[0m[0;34m,[0m [0mtobam_cl[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 156[0m do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None, | |
| [0;32m--> 157[0;31m [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)]) | |
| [0m[1;32m 158[0m [0;32mreturn[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 159[0m [0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36mrun[0;34m(cmd, descr, data, checks, region, log_error, log_stdout)[0m | |
| [1;32m 19[0m [0;32mtry[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 20[0m [0mlogger_cl[0m[0;34m.[0m[0mdebug[0m[0;34m([0m[0;34m" "[0m[0;34m.[0m[0mjoin[0m[0;34m([0m[0mstr[0m[0;34m([0m[0mx[0m[0;34m)[0m [0;32mfor[0m [0mx[0m [0;32min[0m [0mcmd[0m[0;34m)[0m [0;32mif[0m [0;32mnot[0m [0misinstance[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mbasestring[0m[0;34m)[0m [0;32melse[0m [0mcmd[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 21[0;31m [0m_do_run[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mchecks[0m[0;34m,[0m [0mlog_stdout[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 22[0m [0;32mexcept[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 23[0m [0mdiagnostics[0m[0;34m.[0m[0mend_cmd[0m[0;34m([0m[0mcmd_id[0m[0;34m,[0m [0mFalse[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36m_do_run[0;34m(cmd, checks, log_stdout)[0m | |
| [1;32m 93[0m [0ms[0m[0;34m.[0m[0mcommunicate[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 94[0m [0ms[0m[0;34m.[0m[0mstdout[0m[0;34m.[0m[0mclose[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 95[0;31m [0;32mraise[0m [0msubprocess[0m[0;34m.[0m[0mCalledProcessError[0m[0;34m([0m[0mexitcode[0m[0;34m,[0m [0merror_msg[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 96[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 97[0m [0;32mbreak[0m[0;34m[0m[0m | |
| [0;31mCalledProcessError[0m: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-2\tPL:illumina\tPU:NA12878-2\tSM:NA12878-2' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 20000001 40000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 20000001 40000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/d2beeaec-fd74-4579-b6a5-b7c5b90526f0/tmpG7iiH8/NA12878-2-sort-20000001_40000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/981265dc-2028-4a1b-9cd3-9edbeef33c78/tmp7kSXXE/NA12878-2-sort-20000001_40000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/d2beeaec-fd74-4579-b6a5-b7c5b90526f0/tmpG7iiH8/NA12878-2-sort-20000001_40000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/59907c84-0d2d-40bd-bf8f-3f3d90706fd8/tmpJzwlnk/NA12878-2-sort-20000001_40000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/d2beeaec-fd74-4579-b6a5-b7c5b90526f0/tmpG7iiH8/NA12878-2-sort-20000001_40000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/d2beeaec-fd74-4579-b6a5-b7c5b90526f0/tmpG7iiH8/NA12878-2-sort-20000001_40000000.bam /dev/stdin | |
| samblaster: Version 0.1.22 | |
| samblaster: Inputting from stdin | |
| samblaster: Outputting to stdout | |
| samblaster: Opening /dev/fd/62 for write. | |
| samblaster: Opening /dev/fd/63 for write. | |
| [W::bseq_read] the 2nd file has fewer sequences. | |
| [M::mem_pestat] skip orientation FF as there are not enough pairs | |
| [M::mem_pestat] skip orientation FR as there are not enough pairs | |
| [M::mem_pestat] skip orientation RF as there are not enough pairs | |
| [M::mem_pestat] skip orientation RR as there are not enough pairs | |
| [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1106:12361:170167", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170" | |
| [mem_sam_pe] samblaster: Loaded 84 header sequence entries. | |
| ' returned non-zero exit status 1 | |
| cat: write error: Broken pipe | |
| 2016-07-28 00:20:46.480 [IPEngineApp] Exception in apply request: | |
| [0;31m[0m | |
| [0;31mCalledProcessError[0mTraceback (most recent call last) | |
| [0;32m<string>[0m in [0;36m<module>[0;34m()[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc[0m in [0;36m__call__[0;34m(self, *args, **kwargs)[0m | |
| [1;32m 71[0m [0;34m[0m[0m | |
| [1;32m 72[0m [0;32mdef[0m [0m__call__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m---> 73[0;31m [0;32mreturn[0m [0mself[0m[0;34m.[0m[0mf[0m[0;34m([0m[0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 74[0m [0;34m[0m[0m | |
| [1;32m 75[0m [0;32mif[0m [0;32mnot[0m [0mpy3compat[0m[0;34m.[0m[0mPY3[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc[0m in [0;36mprocess_alignment[0;34m(*args)[0m | |
| [1;32m 179[0m [0margs[0m [0;34m=[0m [0mipython[0m[0;34m.[0m[0munzip_args[0m[0;34m([0m[0margs[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 180[0m [0;32mwith[0m [0m_setup_logging[0m[0;34m([0m[0margs[0m[0;34m)[0m [0;32mas[0m [0mconfig[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m--> 181[0;31m [0;32mreturn[0m [0mipython[0m[0;34m.[0m[0mzip_args[0m[0;34m([0m[0mapply[0m[0;34m([0m[0msample[0m[0;34m.[0m[0mprocess_alignment[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 182[0m [0;34m[0m[0m | |
| [1;32m 183[0m [0;34m@[0m[0mrequire[0m[0;34m([0m[0malignprep[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc[0m in [0;36mprocess_alignment[0;34m(data, alt_input)[0m | |
| [1;32m 110[0m [0;32mif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0maligner[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 111[0m [0mlogger[0m[0;34m.[0m[0minfo[0m[0;34m([0m[0;34m"Aligning lane %s with %s aligner"[0m [0;34m%[0m [0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"rgnames"[0m[0;34m][0m[0;34m[[0m[0;34m"lane"[0m[0;34m][0m[0;34m,[0m [0maligner[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m--> 112[0;31m [0mdata[0m [0;34m=[0m [0malign_to_sort_bam[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0maligner[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 113[0m [0mdata[0m [0;34m=[0m [0m_add_supplemental_bams[0m[0;34m([0m[0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 114[0m [0;32melif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0mfastq1[0m[0;34m.[0m[0mendswith[0m[0;34m([0m[0;34m".bam"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36malign_to_sort_bam[0;34m(fastq1, fastq2, aligner, data)[0m | |
| [1;32m 62[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 63[0m data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file, | |
| [0;32m---> 64[0;31m names, align_dir, data) | |
| [0m[1;32m 65[0m [0;32mif[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;32mand[0m [0mutils[0m[0;34m.[0m[0mfile_exists[0m[0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 66[0m [0;32mif[0m [0;32mnot[0m [0mdata[0m[0;34m.[0m[0mget[0m[0;34m([0m[0;34m"align_split"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36m_align_from_fastq[0;34m(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)[0m | |
| [1;32m 115[0m [0mconfig[0m [0;34m=[0m [0mdata[0m[0;34m[[0m[0;34m"config"[0m[0;34m][0m[0;34m[0m[0m | |
| [1;32m 116[0m [0malign_fn[0m [0;34m=[0m [0mTOOLS[0m[0;34m[[0m[0maligner[0m[0;34m][0m[0;34m.[0m[0malign_fn[0m[0;34m[0m[0m | |
| [0;32m--> 117[0;31m [0mout[0m [0;34m=[0m [0malign_fn[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0malign_ref[0m[0;34m,[0m [0mnames[0m[0;34m,[0m [0malign_dir[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 118[0m [0;31m# handle align functions that update the main data dictionary in place[0m[0;34m[0m[0;34m[0m[0m | |
| [1;32m 119[0m [0;32mif[0m [0misinstance[0m[0;34m([0m[0mout[0m[0;34m,[0m [0mdict[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36malign_pipe[0;34m(fastq_file, pair_file, ref_file, names, align_dir, data)[0m | |
| [1;32m 145[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 146[0m out_file = _align_mem(fastq_file, pair_file, ref_file, out_file, | |
| [0;32m--> 147[0;31m names, rg_info, data) | |
| [0m[1;32m 148[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;34m=[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 149[0m [0;32mreturn[0m [0mdata[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36m_align_mem[0;34m(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)[0m | |
| [1;32m 155[0m [0mcmd[0m [0;34m=[0m [0;34m"%s | %s"[0m [0;34m%[0m [0;34m([0m[0m_get_bwa_mem_cmd[0m[0;34m([0m[0mdata[0m[0;34m,[0m [0mout_file[0m[0;34m,[0m [0mref_file[0m[0;34m,[0m [0mfastq_file[0m[0;34m,[0m [0mpair_file[0m[0;34m)[0m[0;34m,[0m [0mtobam_cl[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 156[0m do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None, | |
| [0;32m--> 157[0;31m [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)]) | |
| [0m[1;32m 158[0m [0;32mreturn[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 159[0m [0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36mrun[0;34m(cmd, descr, data, checks, region, log_error, log_stdout)[0m | |
| [1;32m 19[0m [0;32mtry[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 20[0m [0mlogger_cl[0m[0;34m.[0m[0mdebug[0m[0;34m([0m[0;34m" "[0m[0;34m.[0m[0mjoin[0m[0;34m([0m[0mstr[0m[0;34m([0m[0mx[0m[0;34m)[0m [0;32mfor[0m [0mx[0m [0;32min[0m [0mcmd[0m[0;34m)[0m [0;32mif[0m [0;32mnot[0m [0misinstance[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mbasestring[0m[0;34m)[0m [0;32melse[0m [0mcmd[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 21[0;31m [0m_do_run[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mchecks[0m[0;34m,[0m [0mlog_stdout[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 22[0m [0;32mexcept[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 23[0m [0mdiagnostics[0m[0;34m.[0m[0mend_cmd[0m[0;34m([0m[0mcmd_id[0m[0;34m,[0m [0mFalse[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36m_do_run[0;34m(cmd, checks, log_stdout)[0m | |
| [1;32m 93[0m [0ms[0m[0;34m.[0m[0mcommunicate[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 94[0m [0ms[0m[0;34m.[0m[0mstdout[0m[0;34m.[0m[0mclose[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 95[0;31m [0;32mraise[0m [0msubprocess[0m[0;34m.[0m[0mCalledProcessError[0m[0;34m([0m[0mexitcode[0m[0;34m,[0m [0merror_msg[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 96[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 97[0m [0;32mbreak[0m[0;34m[0m[0m | |
| [0;31mCalledProcessError[0m: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-2\tPL:illumina\tPU:NA12878-2\tSM:NA12878-2' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 40000001 60000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 40000001 60000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/c836662c-9579-4938-bd8e-fbb2b4069414/tmpIHJrp5/NA12878-2-sort-40000001_60000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/b77edd90-f94c-4ba3-aa8e-11f65610e826/tmpRb3Fg2/NA12878-2-sort-40000001_60000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/c836662c-9579-4938-bd8e-fbb2b4069414/tmpIHJrp5/NA12878-2-sort-40000001_60000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/ee37cf82-ec3f-4c56-a3f1-ee0e3a7088e7/tmpmMqMrM/NA12878-2-sort-40000001_60000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/c836662c-9579-4938-bd8e-fbb2b4069414/tmpIHJrp5/NA12878-2-sort-40000001_60000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/c836662c-9579-4938-bd8e-fbb2b4069414/tmpIHJrp5/NA12878-2-sort-40000001_60000000.bam /dev/stdin | |
| samblaster: Version 0.1.22 | |
| samblaster: Inputting from stdin | |
| samblaster: Outputting to stdout | |
| samblaster: Opening /dev/fd/62 for write. | |
| samblaster: Opening /dev/fd/63 for write. | |
| [W::bseq_read] the 2nd file has fewer sequences. | |
| [M::mem_pestat] skip orientation FF as there are not enough pairs | |
| [M::mem_pestat] skip orientation FR as there are not enough pairs | |
| [M::mem_pestat] skip orientation RF as there are not enough pairs | |
| [M::mem_pestat] skip orientation RR as there are not enough pairs | |
| [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1204:16327:72117", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170" | |
| [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1204:16388:72120", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170" | |
| [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1204:16597:72069", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170" | |
| samblaster: Loaded 84 header sequence entries. | |
| ' returned non-zero exit status 1 | |
| cat: write error: Broken pipe | |
| 2016-07-28 00:21:37.050 [IPEngineApp] Exception in apply request: | |
| [0;31m[0m | |
| [0;31mCalledProcessError[0mTraceback (most recent call last) | |
| [0;32m<string>[0m in [0;36m<module>[0;34m()[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc[0m in [0;36m__call__[0;34m(self, *args, **kwargs)[0m | |
| [1;32m 71[0m [0;34m[0m[0m | |
| [1;32m 72[0m [0;32mdef[0m [0m__call__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m---> 73[0;31m [0;32mreturn[0m [0mself[0m[0;34m.[0m[0mf[0m[0;34m([0m[0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 74[0m [0;34m[0m[0m | |
| [1;32m 75[0m [0;32mif[0m [0;32mnot[0m [0mpy3compat[0m[0;34m.[0m[0mPY3[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc[0m in [0;36mprocess_alignment[0;34m(*args)[0m | |
| [1;32m 179[0m [0margs[0m [0;34m=[0m [0mipython[0m[0;34m.[0m[0munzip_args[0m[0;34m([0m[0margs[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 180[0m [0;32mwith[0m [0m_setup_logging[0m[0;34m([0m[0margs[0m[0;34m)[0m [0;32mas[0m [0mconfig[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m--> 181[0;31m [0;32mreturn[0m [0mipython[0m[0;34m.[0m[0mzip_args[0m[0;34m([0m[0mapply[0m[0;34m([0m[0msample[0m[0;34m.[0m[0mprocess_alignment[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 182[0m [0;34m[0m[0m | |
| [1;32m 183[0m [0;34m@[0m[0mrequire[0m[0;34m([0m[0malignprep[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc[0m in [0;36mprocess_alignment[0;34m(data, alt_input)[0m | |
| [1;32m 110[0m [0;32mif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0maligner[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 111[0m [0mlogger[0m[0;34m.[0m[0minfo[0m[0;34m([0m[0;34m"Aligning lane %s with %s aligner"[0m [0;34m%[0m [0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"rgnames"[0m[0;34m][0m[0;34m[[0m[0;34m"lane"[0m[0;34m][0m[0;34m,[0m [0maligner[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m--> 112[0;31m [0mdata[0m [0;34m=[0m [0malign_to_sort_bam[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0maligner[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 113[0m [0mdata[0m [0;34m=[0m [0m_add_supplemental_bams[0m[0;34m([0m[0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 114[0m [0;32melif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0mfastq1[0m[0;34m.[0m[0mendswith[0m[0;34m([0m[0;34m".bam"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36malign_to_sort_bam[0;34m(fastq1, fastq2, aligner, data)[0m | |
| [1;32m 62[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 63[0m data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file, | |
| [0;32m---> 64[0;31m names, align_dir, data) | |
| [0m[1;32m 65[0m [0;32mif[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;32mand[0m [0mutils[0m[0;34m.[0m[0mfile_exists[0m[0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 66[0m [0;32mif[0m [0;32mnot[0m [0mdata[0m[0;34m.[0m[0mget[0m[0;34m([0m[0;34m"align_split"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36m_align_from_fastq[0;34m(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)[0m | |
| [1;32m 115[0m [0mconfig[0m [0;34m=[0m [0mdata[0m[0;34m[[0m[0;34m"config"[0m[0;34m][0m[0;34m[0m[0m | |
| [1;32m 116[0m [0malign_fn[0m [0;34m=[0m [0mTOOLS[0m[0;34m[[0m[0maligner[0m[0;34m][0m[0;34m.[0m[0malign_fn[0m[0;34m[0m[0m | |
| [0;32m--> 117[0;31m [0mout[0m [0;34m=[0m [0malign_fn[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0malign_ref[0m[0;34m,[0m [0mnames[0m[0;34m,[0m [0malign_dir[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 118[0m [0;31m# handle align functions that update the main data dictionary in place[0m[0;34m[0m[0;34m[0m[0m | |
| [1;32m 119[0m [0;32mif[0m [0misinstance[0m[0;34m([0m[0mout[0m[0;34m,[0m [0mdict[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36malign_pipe[0;34m(fastq_file, pair_file, ref_file, names, align_dir, data)[0m | |
| [1;32m 145[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 146[0m out_file = _align_mem(fastq_file, pair_file, ref_file, out_file, | |
| [0;32m--> 147[0;31m names, rg_info, data) | |
| [0m[1;32m 148[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;34m=[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 149[0m [0;32mreturn[0m [0mdata[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36m_align_mem[0;34m(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)[0m | |
| [1;32m 155[0m [0mcmd[0m [0;34m=[0m [0;34m"%s | %s"[0m [0;34m%[0m [0;34m([0m[0m_get_bwa_mem_cmd[0m[0;34m([0m[0mdata[0m[0;34m,[0m [0mout_file[0m[0;34m,[0m [0mref_file[0m[0;34m,[0m [0mfastq_file[0m[0;34m,[0m [0mpair_file[0m[0;34m)[0m[0;34m,[0m [0mtobam_cl[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 156[0m do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None, | |
| [0;32m--> 157[0;31m [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)]) | |
| [0m[1;32m 158[0m [0;32mreturn[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 159[0m [0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36mrun[0;34m(cmd, descr, data, checks, region, log_error, log_stdout)[0m | |
| [1;32m 19[0m [0;32mtry[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 20[0m [0mlogger_cl[0m[0;34m.[0m[0mdebug[0m[0;34m([0m[0;34m" "[0m[0;34m.[0m[0mjoin[0m[0;34m([0m[0mstr[0m[0;34m([0m[0mx[0m[0;34m)[0m [0;32mfor[0m [0mx[0m [0;32min[0m [0mcmd[0m[0;34m)[0m [0;32mif[0m [0;32mnot[0m [0misinstance[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mbasestring[0m[0;34m)[0m [0;32melse[0m [0mcmd[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 21[0;31m [0m_do_run[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mchecks[0m[0;34m,[0m [0mlog_stdout[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 22[0m [0;32mexcept[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 23[0m [0mdiagnostics[0m[0;34m.[0m[0mend_cmd[0m[0;34m([0m[0mcmd_id[0m[0;34m,[0m [0mFalse[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36m_do_run[0;34m(cmd, checks, log_stdout)[0m | |
| [1;32m 93[0m [0ms[0m[0;34m.[0m[0mcommunicate[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 94[0m [0ms[0m[0;34m.[0m[0mstdout[0m[0;34m.[0m[0mclose[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 95[0;31m [0;32mraise[0m [0msubprocess[0m[0;34m.[0m[0mCalledProcessError[0m[0;34m([0m[0mexitcode[0m[0;34m,[0m [0merror_msg[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 96[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 97[0m [0;32mbreak[0m[0;34m[0m[0m | |
| [0;31mCalledProcessError[0m: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-2\tPL:illumina\tPU:NA12878-2\tSM:NA12878-2' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 60000001 80000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 60000001 80000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/eb8fc8d3-9265-45fc-a69b-8d42bfba0d64/tmpaPKyWK/NA12878-2-sort-60000001_80000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/fb87f8e7-1a9f-4ab4-974c-fb20fb590d1d/tmpmHTlgw/NA12878-2-sort-60000001_80000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/eb8fc8d3-9265-45fc-a69b-8d42bfba0d64/tmpaPKyWK/NA12878-2-sort-60000001_80000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/b4dbf326-b367-4c1f-8e3d-f15c9a7b6564/tmpsGM7Zh/NA12878-2-sort-60000001_80000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/eb8fc8d3-9265-45fc-a69b-8d42bfba0d64/tmpaPKyWK/NA12878-2-sort-60000001_80000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/eb8fc8d3-9265-45fc-a69b-8d42bfba0d64/tmpaPKyWK/NA12878-2-sort-60000001_80000000.bam /dev/stdin | |
| samblaster: Version 0.1.22 | |
| samblaster: Inputting from stdin | |
| samblaster: Outputting to stdout | |
| samblaster: Opening /dev/fd/62 for write. | |
| samblaster: Opening /dev/fd/63 for write. | |
| [M::mem_pestat] skip orientation FF as there are not enough pairs | |
| [M::mem_pestat] skip orientation FR as there are not enough pairs | |
| [M::mem_pestat] skip orientation RF as there are not enough pairs | |
| [M::mem_pestat] skip orientation RR as there are not enough pairs | |
| [mem_sam_pe] [mem_sam_pe] [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1301:20180:104496", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170" | |
| [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1301:20388:104287", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170" | |
| [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1301:20287:104306", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170" | |
| [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1301:20615:104279", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170" | |
| paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1301:20315:104460", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170" | |
| [mem_sam_pe] | |
| paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1301:20356:104489", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170" | |
| paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1301:20162:104468", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170" | |
| [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1301:20460:104376", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170" | |
| [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1301:20279:104265", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170" | |
| samblaster: Loaded 84 header sequence entries. | |
| ' returned non-zero exit status 1 | |
| cat: write error: Broken pipe | |
| 2016-07-28 00:21:58.797 [IPEngineApp] Exception in apply request: | |
| [0;31m[0m | |
| [0;31mCalledProcessError[0mTraceback (most recent call last) | |
| [0;32m<string>[0m in [0;36m<module>[0;34m()[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc[0m in [0;36m__call__[0;34m(self, *args, **kwargs)[0m | |
| [1;32m 71[0m [0;34m[0m[0m | |
| [1;32m 72[0m [0;32mdef[0m [0m__call__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m---> 73[0;31m [0;32mreturn[0m [0mself[0m[0;34m.[0m[0mf[0m[0;34m([0m[0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 74[0m [0;34m[0m[0m | |
| [1;32m 75[0m [0;32mif[0m [0;32mnot[0m [0mpy3compat[0m[0;34m.[0m[0mPY3[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc[0m in [0;36mprocess_alignment[0;34m(*args)[0m | |
| [1;32m 179[0m [0margs[0m [0;34m=[0m [0mipython[0m[0;34m.[0m[0munzip_args[0m[0;34m([0m[0margs[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 180[0m [0;32mwith[0m [0m_setup_logging[0m[0;34m([0m[0margs[0m[0;34m)[0m [0;32mas[0m [0mconfig[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m--> 181[0;31m [0;32mreturn[0m [0mipython[0m[0;34m.[0m[0mzip_args[0m[0;34m([0m[0mapply[0m[0;34m([0m[0msample[0m[0;34m.[0m[0mprocess_alignment[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 182[0m [0;34m[0m[0m | |
| [1;32m 183[0m [0;34m@[0m[0mrequire[0m[0;34m([0m[0malignprep[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc[0m in [0;36mprocess_alignment[0;34m(data, alt_input)[0m | |
| [1;32m 110[0m [0;32mif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0maligner[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 111[0m [0mlogger[0m[0;34m.[0m[0minfo[0m[0;34m([0m[0;34m"Aligning lane %s with %s aligner"[0m [0;34m%[0m [0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"rgnames"[0m[0;34m][0m[0;34m[[0m[0;34m"lane"[0m[0;34m][0m[0;34m,[0m [0maligner[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m--> 112[0;31m [0mdata[0m [0;34m=[0m [0malign_to_sort_bam[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0maligner[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 113[0m [0mdata[0m [0;34m=[0m [0m_add_supplemental_bams[0m[0;34m([0m[0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 114[0m [0;32melif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0mfastq1[0m[0;34m.[0m[0mendswith[0m[0;34m([0m[0;34m".bam"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36malign_to_sort_bam[0;34m(fastq1, fastq2, aligner, data)[0m | |
| [1;32m 62[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 63[0m data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file, | |
| [0;32m---> 64[0;31m names, align_dir, data) | |
| [0m[1;32m 65[0m [0;32mif[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;32mand[0m [0mutils[0m[0;34m.[0m[0mfile_exists[0m[0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 66[0m [0;32mif[0m [0;32mnot[0m [0mdata[0m[0;34m.[0m[0mget[0m[0;34m([0m[0;34m"align_split"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36m_align_from_fastq[0;34m(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)[0m | |
| [1;32m 115[0m [0mconfig[0m [0;34m=[0m [0mdata[0m[0;34m[[0m[0;34m"config"[0m[0;34m][0m[0;34m[0m[0m | |
| [1;32m 116[0m [0malign_fn[0m [0;34m=[0m [0mTOOLS[0m[0;34m[[0m[0maligner[0m[0;34m][0m[0;34m.[0m[0malign_fn[0m[0;34m[0m[0m | |
| [0;32m--> 117[0;31m [0mout[0m [0;34m=[0m [0malign_fn[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0malign_ref[0m[0;34m,[0m [0mnames[0m[0;34m,[0m [0malign_dir[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 118[0m [0;31m# handle align functions that update the main data dictionary in place[0m[0;34m[0m[0;34m[0m[0m | |
| [1;32m 119[0m [0;32mif[0m [0misinstance[0m[0;34m([0m[0mout[0m[0;34m,[0m [0mdict[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36malign_pipe[0;34m(fastq_file, pair_file, ref_file, names, align_dir, data)[0m | |
| [1;32m 145[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 146[0m out_file = _align_mem(fastq_file, pair_file, ref_file, out_file, | |
| [0;32m--> 147[0;31m names, rg_info, data) | |
| [0m[1;32m 148[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;34m=[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 149[0m [0;32mreturn[0m [0mdata[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36m_align_mem[0;34m(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)[0m | |
| [1;32m 155[0m [0mcmd[0m [0;34m=[0m [0;34m"%s | %s"[0m [0;34m%[0m [0;34m([0m[0m_get_bwa_mem_cmd[0m[0;34m([0m[0mdata[0m[0;34m,[0m [0mout_file[0m[0;34m,[0m [0mref_file[0m[0;34m,[0m [0mfastq_file[0m[0;34m,[0m [0mpair_file[0m[0;34m)[0m[0;34m,[0m [0mtobam_cl[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 156[0m do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None, | |
| [0;32m--> 157[0;31m [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)]) | |
| [0m[1;32m 158[0m [0;32mreturn[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 159[0m [0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36mrun[0;34m(cmd, descr, data, checks, region, log_error, log_stdout)[0m | |
| [1;32m 19[0m [0;32mtry[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 20[0m [0mlogger_cl[0m[0;34m.[0m[0mdebug[0m[0;34m([0m[0;34m" "[0m[0;34m.[0m[0mjoin[0m[0;34m([0m[0mstr[0m[0;34m([0m[0mx[0m[0;34m)[0m [0;32mfor[0m [0mx[0m [0;32min[0m [0mcmd[0m[0;34m)[0m [0;32mif[0m [0;32mnot[0m [0misinstance[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mbasestring[0m[0;34m)[0m [0;32melse[0m [0mcmd[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 21[0;31m [0m_do_run[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mchecks[0m[0;34m,[0m [0mlog_stdout[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 22[0m [0;32mexcept[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 23[0m [0mdiagnostics[0m[0;34m.[0m[0mend_cmd[0m[0;34m([0m[0mcmd_id[0m[0;34m,[0m [0mFalse[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36m_do_run[0;34m(cmd, checks, log_stdout)[0m | |
| [1;32m 93[0m [0ms[0m[0;34m.[0m[0mcommunicate[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 94[0m [0ms[0m[0;34m.[0m[0mstdout[0m[0;34m.[0m[0mclose[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 95[0;31m [0;32mraise[0m [0msubprocess[0m[0;34m.[0m[0mCalledProcessError[0m[0;34m([0m[0mexitcode[0m[0;34m,[0m [0merror_msg[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 96[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 97[0m [0;32mbreak[0m[0;34m[0m[0m | |
| [0;31mCalledProcessError[0m: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-2\tPL:illumina\tPU:NA12878-2\tSM:NA12878-2' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 80000001 100000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 80000001 100000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/b043c4a9-af9f-46e3-904a-4ea2b3e76795/tmpzWC3G6/NA12878-2-sort-80000001_100000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/a8252421-66ad-4cba-8ce3-b58294ade9d2/tmp9sLFs9/NA12878-2-sort-80000001_100000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/b043c4a9-af9f-46e3-904a-4ea2b3e76795/tmpzWC3G6/NA12878-2-sort-80000001_100000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/ee95b147-150d-4d5f-91e1-a2266236a8de/tmpSCdWLu/NA12878-2-sort-80000001_100000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/b043c4a9-af9f-46e3-904a-4ea2b3e76795/tmpzWC3G6/NA12878-2-sort-80000001_100000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/b043c4a9-af9f-46e3-904a-4ea2b3e76795/tmpzWC3G6/NA12878-2-sort-80000001_100000000.bam /dev/stdin | |
| duplicating @SQ line GL000199.1 | |
| duplicating @SQ line GL000217.1 | |
| duplicating @SQ line GL000216.1 | |
| duplicating @SQ line GL000215.1 | |
| duplicating @SQ line GL000205.1 | |
| duplicating @SQ line GL000219.1 | |
| duplicating @SQ line GL000224.1 | |
| duplicating @SQ line GL000223.1 | |
| duplicating @SQ line GL000195.1 | |
| duplicating @SQ line GL000212.1 | |
| duplicating @SQ line GL000222.1 | |
| duplicating @SQ line GL000200.1 | |
| duplicating @SQ line GL000193.1 | |
| duplicating @SQ line GL000194.1 | |
| duplicating @SQ line GL000225.1 | |
| duplicating @SQ line GL000192.1 | |
| duplicating @SQ line 1 | |
| duplicating @SQ line 2 | |
| duplicating @SQ line 3 | |
| duplicating @SQ line 4 | |
| duplicating @SQ line 5 | |
| duplicating @SQ line 6 | |
| duplicating @SQ line 7 | |
| duplicating @SQ line 8 | |
| duplicating @SQ line 9 | |
| duplicating @SQ line 10 | |
| duplicating @SQ line 11 | |
| duplicating @SQ line 12 | |
| duplicating @SQ line 13 | |
| duplicating @SQ line 14 | |
| duplicating @SQ line 15 | |
| duplicating @SQ line 16 | |
| duplicating @SQ line 17 | |
| duplicating @SQ line 18 | |
| duplicating @SQ line 19 | |
| duplicating @SQ line 20 | |
| duplicating @SQ line 21 | |
| duplicating @SQ line 22 | |
| duplicating @SQ line X | |
| duplicating @SQ line Y | |
| duplicating @SQ line MT | |
| duplicating @SQ line GL000207.1 | |
| duplicating @SQ line GL000226.1 | |
| duplicating @SQ line GL000229.1 | |
| duplicating @SQ line GL000231.1 | |
| duplicating @SQ line GL000210.1 | |
| duplicating @SQ line GL000239.1 | |
| duplicating @SQ line GL000235.1 | |
| duplicating @SQ line GL000201.1 | |
| duplicating @SQ line GL000247.1 | |
| duplicating @SQ line GL000245.1 | |
| duplicating @SQ line GL000197.1 | |
| duplicating @SQ line GL000203.1 | |
| duplicating @SQ line GL000246.1 | |
| duplicating @SQ line GL000249.1 | |
| duplicating @SQ line GL000196.1 | |
| duplicating @SQ line GL000248.1 | |
| duplicating @SQ line GL000244.1 | |
| duplicating @SQ line GL000238.1 | |
| duplicating @SQ line GL000202.1 | |
| duplicating @SQ line GL000234.1 | |
| duplicating @SQ line GL000232.1 | |
| duplicating @SQ line GL000206.1 | |
| duplicating @SQ line GL000240.1 | |
| duplicating @SQ line GL000236.1 | |
| duplicating @SQ line GL000241.1 | |
| duplicating @SQ line GL000243.1 | |
| duplicating @SQ line GL000242.1 | |
| duplicating @SQ line GL000230.1 | |
| duplicating @SQ line GL000237.1 | |
| duplicating @SQ line GL000233.1 | |
| duplicating @SQ line GL000204.1 | |
| duplicating @SQ line GL000198.1 | |
| duplicating @SQ line GL000208.1 | |
| duplicating @SQ line GL000191.1 | |
| duplicating @SQ line GL000227.1 | |
| duplicating @SQ line GL000228.1 | |
| duplicating @SQ line GL000214.1 | |
| duplicating @SQ line GL000221.1 | |
| duplicating @SQ line GL000209.1 | |
| duplicating @SQ line GL000218.1 | |
| duplicating @SQ line GL000220.1 | |
| duplicating @SQ line GL000213.1 | |
| duplicating @SQ line GL000211.1 | |
| duplicating @SQ line GL000199.1 | |
| duplicating @SQ line GL000217.1 | |
| duplicating @SQ line GL000216.1 | |
| duplicating @SQ line GL000215.1 | |
| duplicating @SQ line GL000205.1 | |
| duplicating @SQ line GL000219.1 | |
| duplicating @SQ line GL000224.1 | |
| duplicating @SQ line GL000223.1 | |
| duplicating @SQ line GL000195.1 | |
| duplicating @SQ line GL000212.1 | |
| duplicating @SQ line GL000222.1 | |
| duplicating @SQ line GL000200.1 | |
| duplicating @SQ line GL000193.1 | |
| duplicating @SQ line GL000194.1 | |
| duplicating @SQ line GL000225.1 | |
| duplicating @SQ line GL000192.1 | |
| ' returned non-zero exit status 1 | |
| cat: write error: Broken pipe | |
| 2016-07-28 00:22:20.649 [IPEngineApp] Exception in apply request: | |
| [0;31m[0m | |
| [0;31mCalledProcessError[0mTraceback (most recent call last) | |
| [0;32m<string>[0m in [0;36m<module>[0;34m()[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc[0m in [0;36m__call__[0;34m(self, *args, **kwargs)[0m | |
| [1;32m 71[0m [0;34m[0m[0m | |
| [1;32m 72[0m [0;32mdef[0m [0m__call__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m---> 73[0;31m [0;32mreturn[0m [0mself[0m[0;34m.[0m[0mf[0m[0;34m([0m[0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 74[0m [0;34m[0m[0m | |
| [1;32m 75[0m [0;32mif[0m [0;32mnot[0m [0mpy3compat[0m[0;34m.[0m[0mPY3[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc[0m in [0;36mprocess_alignment[0;34m(*args)[0m | |
| [1;32m 179[0m [0margs[0m [0;34m=[0m [0mipython[0m[0;34m.[0m[0munzip_args[0m[0;34m([0m[0margs[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 180[0m [0;32mwith[0m [0m_setup_logging[0m[0;34m([0m[0margs[0m[0;34m)[0m [0;32mas[0m [0mconfig[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m--> 181[0;31m [0;32mreturn[0m [0mipython[0m[0;34m.[0m[0mzip_args[0m[0;34m([0m[0mapply[0m[0;34m([0m[0msample[0m[0;34m.[0m[0mprocess_alignment[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 182[0m [0;34m[0m[0m | |
| [1;32m 183[0m [0;34m@[0m[0mrequire[0m[0;34m([0m[0malignprep[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc[0m in [0;36mprocess_alignment[0;34m(data, alt_input)[0m | |
| [1;32m 110[0m [0;32mif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0maligner[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 111[0m [0mlogger[0m[0;34m.[0m[0minfo[0m[0;34m([0m[0;34m"Aligning lane %s with %s aligner"[0m [0;34m%[0m [0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"rgnames"[0m[0;34m][0m[0;34m[[0m[0;34m"lane"[0m[0;34m][0m[0;34m,[0m [0maligner[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m--> 112[0;31m [0mdata[0m [0;34m=[0m [0malign_to_sort_bam[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0maligner[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 113[0m [0mdata[0m [0;34m=[0m [0m_add_supplemental_bams[0m[0;34m([0m[0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 114[0m [0;32melif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0mfastq1[0m[0;34m.[0m[0mendswith[0m[0;34m([0m[0;34m".bam"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36malign_to_sort_bam[0;34m(fastq1, fastq2, aligner, data)[0m | |
| [1;32m 62[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 63[0m data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file, | |
| [0;32m---> 64[0;31m names, align_dir, data) | |
| [0m[1;32m 65[0m [0;32mif[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;32mand[0m [0mutils[0m[0;34m.[0m[0mfile_exists[0m[0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 66[0m [0;32mif[0m [0;32mnot[0m [0mdata[0m[0;34m.[0m[0mget[0m[0;34m([0m[0;34m"align_split"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36m_align_from_fastq[0;34m(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)[0m | |
| [1;32m 115[0m [0mconfig[0m [0;34m=[0m [0mdata[0m[0;34m[[0m[0;34m"config"[0m[0;34m][0m[0;34m[0m[0m | |
| [1;32m 116[0m [0malign_fn[0m [0;34m=[0m [0mTOOLS[0m[0;34m[[0m[0maligner[0m[0;34m][0m[0;34m.[0m[0malign_fn[0m[0;34m[0m[0m | |
| [0;32m--> 117[0;31m [0mout[0m [0;34m=[0m [0malign_fn[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0malign_ref[0m[0;34m,[0m [0mnames[0m[0;34m,[0m [0malign_dir[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 118[0m [0;31m# handle align functions that update the main data dictionary in place[0m[0;34m[0m[0;34m[0m[0m | |
| [1;32m 119[0m [0;32mif[0m [0misinstance[0m[0;34m([0m[0mout[0m[0;34m,[0m [0mdict[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36malign_pipe[0;34m(fastq_file, pair_file, ref_file, names, align_dir, data)[0m | |
| [1;32m 145[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 146[0m out_file = _align_mem(fastq_file, pair_file, ref_file, out_file, | |
| [0;32m--> 147[0;31m names, rg_info, data) | |
| [0m[1;32m 148[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;34m=[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 149[0m [0;32mreturn[0m [0mdata[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36m_align_mem[0;34m(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)[0m | |
| [1;32m 155[0m [0mcmd[0m [0;34m=[0m [0;34m"%s | %s"[0m [0;34m%[0m [0;34m([0m[0m_get_bwa_mem_cmd[0m[0;34m([0m[0mdata[0m[0;34m,[0m [0mout_file[0m[0;34m,[0m [0mref_file[0m[0;34m,[0m [0mfastq_file[0m[0;34m,[0m [0mpair_file[0m[0;34m)[0m[0;34m,[0m [0mtobam_cl[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 156[0m do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None, | |
| [0;32m--> 157[0;31m [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)]) | |
| [0m[1;32m 158[0m [0;32mreturn[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 159[0m [0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36mrun[0;34m(cmd, descr, data, checks, region, log_error, log_stdout)[0m | |
| [1;32m 19[0m [0;32mtry[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 20[0m [0mlogger_cl[0m[0;34m.[0m[0mdebug[0m[0;34m([0m[0;34m" "[0m[0;34m.[0m[0mjoin[0m[0;34m([0m[0mstr[0m[0;34m([0m[0mx[0m[0;34m)[0m [0;32mfor[0m [0mx[0m [0;32min[0m [0mcmd[0m[0;34m)[0m [0;32mif[0m [0;32mnot[0m [0misinstance[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mbasestring[0m[0;34m)[0m [0;32melse[0m [0mcmd[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 21[0;31m [0m_do_run[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mchecks[0m[0;34m,[0m [0mlog_stdout[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 22[0m [0;32mexcept[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 23[0m [0mdiagnostics[0m[0;34m.[0m[0mend_cmd[0m[0;34m([0m[0mcmd_id[0m[0;34m,[0m [0mFalse[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36m_do_run[0;34m(cmd, checks, log_stdout)[0m | |
| [1;32m 93[0m [0ms[0m[0;34m.[0m[0mcommunicate[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 94[0m [0ms[0m[0;34m.[0m[0mstdout[0m[0;34m.[0m[0mclose[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 95[0;31m [0;32mraise[0m [0msubprocess[0m[0;34m.[0m[0mCalledProcessError[0m[0;34m([0m[0mexitcode[0m[0;34m,[0m [0merror_msg[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 96[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 97[0m [0;32mbreak[0m[0;34m[0m[0m | |
| [0;31mCalledProcessError[0m: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-2\tPL:illumina\tPU:NA12878-2\tSM:NA12878-2' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 100000001 120000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 100000001 120000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/019bc707-7f20-4b2c-bc72-5c27c8de97a4/tmpbhVMW7/NA12878-2-sort-100000001_120000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/93cc0d04-3311-4891-ae89-e6043a917d59/tmppQu0Kn/NA12878-2-sort-100000001_120000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/019bc707-7f20-4b2c-bc72-5c27c8de97a4/tmpbhVMW7/NA12878-2-sort-100000001_120000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/93a9a601-13d6-44ec-8e40-a614b47ae28b/tmpf9ROae/NA12878-2-sort-100000001_120000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/019bc707-7f20-4b2c-bc72-5c27c8de97a4/tmpbhVMW7/NA12878-2-sort-100000001_120000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/019bc707-7f20-4b2c-bc72-5c27c8de97a4/tmpbhVMW7/NA12878-2-sort-100000001_120000000.bam /dev/stdin | |
| duplicating @SQ line GL000199.1 | |
| duplicating @SQ line GL000217.1 | |
| duplicating @SQ line GL000216.1 | |
| duplicating @SQ line GL000215.1 | |
| duplicating @SQ line GL000205.1 | |
| duplicating @SQ line GL000219.1 | |
| duplicating @SQ line GL000224.1 | |
| duplicating @SQ line GL000223.1 | |
| duplicating @SQ line GL000195.1 | |
| duplicating @SQ line GL000212.1 | |
| duplicating @SQ line GL000222.1 | |
| duplicating @SQ line GL000200.1 | |
| duplicating @SQ line GL000193.1 | |
| duplicating @SQ line GL000194.1 | |
| duplicating @SQ line GL000225.1 | |
| duplicating @SQ line GL000192.1 | |
| duplicating @SQ line 1 | |
| duplicating @SQ line 2 | |
| duplicating @SQ line 3 | |
| duplicating @SQ line 4 | |
| duplicating @SQ line 5 | |
| duplicating @SQ line 6 | |
| duplicating @SQ line 7 | |
| duplicating @SQ line 8 | |
| duplicating @SQ line 9 | |
| duplicating @SQ line 10 | |
| duplicating @SQ line 11 | |
| duplicating @SQ line 12 | |
| duplicating @SQ line 13 | |
| duplicating @SQ line 14 | |
| duplicating @SQ line 15 | |
| duplicating @SQ line 16 | |
| duplicating @SQ line 17 | |
| duplicating @SQ line 18 | |
| duplicating @SQ line 19 | |
| duplicating @SQ line 20 | |
| duplicating @SQ line 21 | |
| duplicating @SQ line 22 | |
| duplicating @SQ line X | |
| duplicating @SQ line Y | |
| duplicating @SQ line MT | |
| duplicating @SQ line GL000207.1 | |
| duplicating @SQ line GL000226.1 | |
| duplicating @SQ line GL000229.1 | |
| duplicating @SQ line GL000231.1 | |
| duplicating @SQ line GL000210.1 | |
| duplicating @SQ line GL000239.1 | |
| duplicating @SQ line GL000235.1 | |
| duplicating @SQ line GL000201.1 | |
| duplicating @SQ line GL000247.1 | |
| duplicating @SQ line GL000245.1 | |
| duplicating @SQ line GL000197.1 | |
| duplicating @SQ line GL000203.1 | |
| duplicating @SQ line GL000246.1 | |
| duplicating @SQ line GL000249.1 | |
| duplicating @SQ line GL000196.1 | |
| duplicating @SQ line GL000248.1 | |
| duplicating @SQ line GL000244.1 | |
| duplicating @SQ line GL000238.1 | |
| duplicating @SQ line GL000202.1 | |
| duplicating @SQ line GL000234.1 | |
| duplicating @SQ line GL000232.1 | |
| duplicating @SQ line GL000206.1 | |
| duplicating @SQ line GL000240.1 | |
| duplicating @SQ line GL000236.1 | |
| duplicating @SQ line GL000241.1 | |
| duplicating @SQ line GL000243.1 | |
| duplicating @SQ line GL000242.1 | |
| duplicating @SQ line GL000230.1 | |
| duplicating @SQ line GL000237.1 | |
| duplicating @SQ line GL000233.1 | |
| duplicating @SQ line GL000204.1 | |
| duplicating @SQ line GL000198.1 | |
| duplicating @SQ line GL000208.1 | |
| duplicating @SQ line GL000191.1 | |
| duplicating @SQ line GL000227.1 | |
| duplicating @SQ line GL000228.1 | |
| duplicating @SQ line GL000214.1 | |
| duplicating @SQ line GL000221.1 | |
| duplicating @SQ line GL000209.1 | |
| duplicating @SQ line GL000218.1 | |
| duplicating @SQ line GL000220.1 | |
| duplicating @SQ line GL000213.1 | |
| duplicating @SQ line GL000211.1 | |
| duplicating @SQ line GL000199.1 | |
| duplicating @SQ line GL000217.1 | |
| duplicating @SQ line GL000216.1 | |
| duplicating @SQ line GL000215.1 | |
| duplicating @SQ line GL000205.1 | |
| duplicating @SQ line GL000219.1 | |
| duplicating @SQ line GL000224.1 | |
| duplicating @SQ line GL000223.1 | |
| duplicating @SQ line GL000195.1 | |
| duplicating @SQ line GL000212.1 | |
| duplicating @SQ line GL000222.1 | |
| duplicating @SQ line GL000200.1 | |
| duplicating @SQ line GL000193.1 | |
| duplicating @SQ line GL000194.1 | |
| duplicating @SQ line GL000225.1 | |
| duplicating @SQ line GL000192.1 | |
| ' returned non-zero exit status 1 | |
| cat: write error: Broken pipe | |
| 2016-07-28 00:23:12.207 [IPEngineApp] Exception in apply request: | |
| [0;31m[0m | |
| [0;31mCalledProcessError[0mTraceback (most recent call last) | |
| [0;32m<string>[0m in [0;36m<module>[0;34m()[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc[0m in [0;36m__call__[0;34m(self, *args, **kwargs)[0m | |
| [1;32m 71[0m [0;34m[0m[0m | |
| [1;32m 72[0m [0;32mdef[0m [0m__call__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m---> 73[0;31m [0;32mreturn[0m [0mself[0m[0;34m.[0m[0mf[0m[0;34m([0m[0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 74[0m [0;34m[0m[0m | |
| [1;32m 75[0m [0;32mif[0m [0;32mnot[0m [0mpy3compat[0m[0;34m.[0m[0mPY3[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc[0m in [0;36mprocess_alignment[0;34m(*args)[0m | |
| [1;32m 179[0m [0margs[0m [0;34m=[0m [0mipython[0m[0;34m.[0m[0munzip_args[0m[0;34m([0m[0margs[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 180[0m [0;32mwith[0m [0m_setup_logging[0m[0;34m([0m[0margs[0m[0;34m)[0m [0;32mas[0m [0mconfig[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m--> 181[0;31m [0;32mreturn[0m [0mipython[0m[0;34m.[0m[0mzip_args[0m[0;34m([0m[0mapply[0m[0;34m([0m[0msample[0m[0;34m.[0m[0mprocess_alignment[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 182[0m [0;34m[0m[0m | |
| [1;32m 183[0m [0;34m@[0m[0mrequire[0m[0;34m([0m[0malignprep[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc[0m in [0;36mprocess_alignment[0;34m(data, alt_input)[0m | |
| [1;32m 110[0m [0;32mif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0maligner[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 111[0m [0mlogger[0m[0;34m.[0m[0minfo[0m[0;34m([0m[0;34m"Aligning lane %s with %s aligner"[0m [0;34m%[0m [0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"rgnames"[0m[0;34m][0m[0;34m[[0m[0;34m"lane"[0m[0;34m][0m[0;34m,[0m [0maligner[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m--> 112[0;31m [0mdata[0m [0;34m=[0m [0malign_to_sort_bam[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0maligner[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 113[0m [0mdata[0m [0;34m=[0m [0m_add_supplemental_bams[0m[0;34m([0m[0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 114[0m [0;32melif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0mfastq1[0m[0;34m.[0m[0mendswith[0m[0;34m([0m[0;34m".bam"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36malign_to_sort_bam[0;34m(fastq1, fastq2, aligner, data)[0m | |
| [1;32m 62[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 63[0m data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file, | |
| [0;32m---> 64[0;31m names, align_dir, data) | |
| [0m[1;32m 65[0m [0;32mif[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;32mand[0m [0mutils[0m[0;34m.[0m[0mfile_exists[0m[0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 66[0m [0;32mif[0m [0;32mnot[0m [0mdata[0m[0;34m.[0m[0mget[0m[0;34m([0m[0;34m"align_split"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36m_align_from_fastq[0;34m(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)[0m | |
| [1;32m 115[0m [0mconfig[0m [0;34m=[0m [0mdata[0m[0;34m[[0m[0;34m"config"[0m[0;34m][0m[0;34m[0m[0m | |
| [1;32m 116[0m [0malign_fn[0m [0;34m=[0m [0mTOOLS[0m[0;34m[[0m[0maligner[0m[0;34m][0m[0;34m.[0m[0malign_fn[0m[0;34m[0m[0m | |
| [0;32m--> 117[0;31m [0mout[0m [0;34m=[0m [0malign_fn[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0malign_ref[0m[0;34m,[0m [0mnames[0m[0;34m,[0m [0malign_dir[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 118[0m [0;31m# handle align functions that update the main data dictionary in place[0m[0;34m[0m[0;34m[0m[0m | |
| [1;32m 119[0m [0;32mif[0m [0misinstance[0m[0;34m([0m[0mout[0m[0;34m,[0m [0mdict[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36malign_pipe[0;34m(fastq_file, pair_file, ref_file, names, align_dir, data)[0m | |
| [1;32m 145[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 146[0m out_file = _align_mem(fastq_file, pair_file, ref_file, out_file, | |
| [0;32m--> 147[0;31m names, rg_info, data) | |
| [0m[1;32m 148[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;34m=[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 149[0m [0;32mreturn[0m [0mdata[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36m_align_mem[0;34m(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)[0m | |
| [1;32m 155[0m [0mcmd[0m [0;34m=[0m [0;34m"%s | %s"[0m [0;34m%[0m [0;34m([0m[0m_get_bwa_mem_cmd[0m[0;34m([0m[0mdata[0m[0;34m,[0m [0mout_file[0m[0;34m,[0m [0mref_file[0m[0;34m,[0m [0mfastq_file[0m[0;34m,[0m [0mpair_file[0m[0;34m)[0m[0;34m,[0m [0mtobam_cl[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 156[0m do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None, | |
| [0;32m--> 157[0;31m [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)]) | |
| [0m[1;32m 158[0m [0;32mreturn[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 159[0m [0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36mrun[0;34m(cmd, descr, data, checks, region, log_error, log_stdout)[0m | |
| [1;32m 19[0m [0;32mtry[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 20[0m [0mlogger_cl[0m[0;34m.[0m[0mdebug[0m[0;34m([0m[0;34m" "[0m[0;34m.[0m[0mjoin[0m[0;34m([0m[0mstr[0m[0;34m([0m[0mx[0m[0;34m)[0m [0;32mfor[0m [0mx[0m [0;32min[0m [0mcmd[0m[0;34m)[0m [0;32mif[0m [0;32mnot[0m [0misinstance[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mbasestring[0m[0;34m)[0m [0;32melse[0m [0mcmd[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 21[0;31m [0m_do_run[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mchecks[0m[0;34m,[0m [0mlog_stdout[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 22[0m [0;32mexcept[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 23[0m [0mdiagnostics[0m[0;34m.[0m[0mend_cmd[0m[0;34m([0m[0mcmd_id[0m[0;34m,[0m [0mFalse[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36m_do_run[0;34m(cmd, checks, log_stdout)[0m | |
| [1;32m 93[0m [0ms[0m[0;34m.[0m[0mcommunicate[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 94[0m [0ms[0m[0;34m.[0m[0mstdout[0m[0;34m.[0m[0mclose[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 95[0;31m [0;32mraise[0m [0msubprocess[0m[0;34m.[0m[0mCalledProcessError[0m[0;34m([0m[0mexitcode[0m[0;34m,[0m [0merror_msg[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 96[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 97[0m [0;32mbreak[0m[0;34m[0m[0m | |
| [0;31mCalledProcessError[0m: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-2\tPL:illumina\tPU:NA12878-2\tSM:NA12878-2' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 120000001 140000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 120000001 140000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/6acef7b1-e644-4023-9b9b-998c9b2de3dc/tmpTRl0G9/NA12878-2-sort-120000001_140000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/e440d58e-f06e-48e9-9ed0-28dadf43ce0a/tmpaAAYTV/NA12878-2-sort-120000001_140000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/6acef7b1-e644-4023-9b9b-998c9b2de3dc/tmpTRl0G9/NA12878-2-sort-120000001_140000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/d792855b-9795-419d-be5e-8da29029b8e7/tmpjVaAhU/NA12878-2-sort-120000001_140000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/6acef7b1-e644-4023-9b9b-998c9b2de3dc/tmpTRl0G9/NA12878-2-sort-120000001_140000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/6acef7b1-e644-4023-9b9b-998c9b2de3dc/tmpTRl0G9/NA12878-2-sort-120000001_140000000.bam /dev/stdin | |
| samblaster: Version 0.1.22 | |
| samblaster: Inputting from stdin | |
| samblaster: Outputting to stdout | |
| samblaster: Opening /dev/fd/62 for write. | |
| samblaster: Opening /dev/fd/63 for write. | |
| [M::mem_pestat] skip orientation FF as there are not enough pairs | |
| [M::mem_pestat] skip orientation FR as there are not enough pairs | |
| [M::mem_pestat] skip orientation RF as there are not enough pairs | |
| [M::mem_pestat] skip orientation RR as there are not enough pairs | |
| [mem_sam_pe] [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:2201:20705:113542", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170" | |
| paired reads have different names: "HWI-ST1124:106:C15APACXX:1:2201:20717:113626", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170" | |
| [mem_sam_pe] samblaster: Loaded 84 header sequence entries. | |
| ' returned non-zero exit status 1 | |
| cat: write error: Broken pipe | |
| 2016-07-28 00:24:04.510 [IPEngineApp] Exception in apply request: | |
| [0;31m[0m | |
| [0;31mCalledProcessError[0mTraceback (most recent call last) | |
| [0;32m<string>[0m in [0;36m<module>[0;34m()[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc[0m in [0;36m__call__[0;34m(self, *args, **kwargs)[0m | |
| [1;32m 71[0m [0;34m[0m[0m | |
| [1;32m 72[0m [0;32mdef[0m [0m__call__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m---> 73[0;31m [0;32mreturn[0m [0mself[0m[0;34m.[0m[0mf[0m[0;34m([0m[0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 74[0m [0;34m[0m[0m | |
| [1;32m 75[0m [0;32mif[0m [0;32mnot[0m [0mpy3compat[0m[0;34m.[0m[0mPY3[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc[0m in [0;36mprocess_alignment[0;34m(*args)[0m | |
| [1;32m 179[0m [0margs[0m [0;34m=[0m [0mipython[0m[0;34m.[0m[0munzip_args[0m[0;34m([0m[0margs[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 180[0m [0;32mwith[0m [0m_setup_logging[0m[0;34m([0m[0margs[0m[0;34m)[0m [0;32mas[0m [0mconfig[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m--> 181[0;31m [0;32mreturn[0m [0mipython[0m[0;34m.[0m[0mzip_args[0m[0;34m([0m[0mapply[0m[0;34m([0m[0msample[0m[0;34m.[0m[0mprocess_alignment[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 182[0m [0;34m[0m[0m | |
| [1;32m 183[0m [0;34m@[0m[0mrequire[0m[0;34m([0m[0malignprep[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc[0m in [0;36mprocess_alignment[0;34m(data, alt_input)[0m | |
| [1;32m 110[0m [0;32mif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0maligner[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 111[0m [0mlogger[0m[0;34m.[0m[0minfo[0m[0;34m([0m[0;34m"Aligning lane %s with %s aligner"[0m [0;34m%[0m [0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"rgnames"[0m[0;34m][0m[0;34m[[0m[0;34m"lane"[0m[0;34m][0m[0;34m,[0m [0maligner[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m--> 112[0;31m [0mdata[0m [0;34m=[0m [0malign_to_sort_bam[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0maligner[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 113[0m [0mdata[0m [0;34m=[0m [0m_add_supplemental_bams[0m[0;34m([0m[0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 114[0m [0;32melif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0mfastq1[0m[0;34m.[0m[0mendswith[0m[0;34m([0m[0;34m".bam"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36malign_to_sort_bam[0;34m(fastq1, fastq2, aligner, data)[0m | |
| [1;32m 62[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 63[0m data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file, | |
| [0;32m---> 64[0;31m names, align_dir, data) | |
| [0m[1;32m 65[0m [0;32mif[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;32mand[0m [0mutils[0m[0;34m.[0m[0mfile_exists[0m[0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 66[0m [0;32mif[0m [0;32mnot[0m [0mdata[0m[0;34m.[0m[0mget[0m[0;34m([0m[0;34m"align_split"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36m_align_from_fastq[0;34m(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)[0m | |
| [1;32m 115[0m [0mconfig[0m [0;34m=[0m [0mdata[0m[0;34m[[0m[0;34m"config"[0m[0;34m][0m[0;34m[0m[0m | |
| [1;32m 116[0m [0malign_fn[0m [0;34m=[0m [0mTOOLS[0m[0;34m[[0m[0maligner[0m[0;34m][0m[0;34m.[0m[0malign_fn[0m[0;34m[0m[0m | |
| [0;32m--> 117[0;31m [0mout[0m [0;34m=[0m [0malign_fn[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0malign_ref[0m[0;34m,[0m [0mnames[0m[0;34m,[0m [0malign_dir[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 118[0m [0;31m# handle align functions that update the main data dictionary in place[0m[0;34m[0m[0;34m[0m[0m | |
| [1;32m 119[0m [0;32mif[0m [0misinstance[0m[0;34m([0m[0mout[0m[0;34m,[0m [0mdict[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36malign_pipe[0;34m(fastq_file, pair_file, ref_file, names, align_dir, data)[0m | |
| [1;32m 145[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 146[0m out_file = _align_mem(fastq_file, pair_file, ref_file, out_file, | |
| [0;32m--> 147[0;31m names, rg_info, data) | |
| [0m[1;32m 148[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;34m=[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 149[0m [0;32mreturn[0m [0mdata[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36m_align_mem[0;34m(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)[0m | |
| [1;32m 155[0m [0mcmd[0m [0;34m=[0m [0;34m"%s | %s"[0m [0;34m%[0m [0;34m([0m[0m_get_bwa_mem_cmd[0m[0;34m([0m[0mdata[0m[0;34m,[0m [0mout_file[0m[0;34m,[0m [0mref_file[0m[0;34m,[0m [0mfastq_file[0m[0;34m,[0m [0mpair_file[0m[0;34m)[0m[0;34m,[0m [0mtobam_cl[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 156[0m do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None, | |
| [0;32m--> 157[0;31m [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)]) | |
| [0m[1;32m 158[0m [0;32mreturn[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 159[0m [0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36mrun[0;34m(cmd, descr, data, checks, region, log_error, log_stdout)[0m | |
| [1;32m 19[0m [0;32mtry[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 20[0m [0mlogger_cl[0m[0;34m.[0m[0mdebug[0m[0;34m([0m[0;34m" "[0m[0;34m.[0m[0mjoin[0m[0;34m([0m[0mstr[0m[0;34m([0m[0mx[0m[0;34m)[0m [0;32mfor[0m [0mx[0m [0;32min[0m [0mcmd[0m[0;34m)[0m [0;32mif[0m [0;32mnot[0m [0misinstance[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mbasestring[0m[0;34m)[0m [0;32melse[0m [0mcmd[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 21[0;31m [0m_do_run[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mchecks[0m[0;34m,[0m [0mlog_stdout[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 22[0m [0;32mexcept[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 23[0m [0mdiagnostics[0m[0;34m.[0m[0mend_cmd[0m[0;34m([0m[0mcmd_id[0m[0;34m,[0m [0mFalse[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36m_do_run[0;34m(cmd, checks, log_stdout)[0m | |
| [1;32m 93[0m [0ms[0m[0;34m.[0m[0mcommunicate[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 94[0m [0ms[0m[0;34m.[0m[0mstdout[0m[0;34m.[0m[0mclose[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 95[0;31m [0;32mraise[0m [0msubprocess[0m[0;34m.[0m[0mCalledProcessError[0m[0;34m([0m[0mexitcode[0m[0;34m,[0m [0merror_msg[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 96[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 97[0m [0;32mbreak[0m[0;34m[0m[0m | |
| [0;31mCalledProcessError[0m: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-2\tPL:illumina\tPU:NA12878-2\tSM:NA12878-2' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 140000001 160000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 140000001 160000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/8e239e80-9d03-4f87-a379-154e8db376da/tmpCbixFJ/NA12878-2-sort-140000001_160000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/be00c357-c469-4c6f-ad58-ef2819779dbc/tmpmDlRz4/NA12878-2-sort-140000001_160000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/8e239e80-9d03-4f87-a379-154e8db376da/tmpCbixFJ/NA12878-2-sort-140000001_160000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/434305af-775e-4e61-8f32-a63845b043dc/tmpLHG6EA/NA12878-2-sort-140000001_160000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/8e239e80-9d03-4f87-a379-154e8db376da/tmpCbixFJ/NA12878-2-sort-140000001_160000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/8e239e80-9d03-4f87-a379-154e8db376da/tmpCbixFJ/NA12878-2-sort-140000001_160000000.bam /dev/stdin | |
| [W::sam_hdr_parse] duplicated sequence 'GL000216.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000215.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000205.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000219.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000224.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000223.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000195.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000212.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000222.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000200.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000193.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000194.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000225.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000192.1' | |
| duplicating @RG line NA12878-2 | |
| duplicating @PG line bwa | |
| duplicating @SQ line 1 | |
| duplicating @SQ line 2 | |
| duplicating @SQ line 3 | |
| duplicating @SQ line 4 | |
| duplicating @SQ line 5 | |
| duplicating @SQ line 6 | |
| duplicating @SQ line 7 | |
| duplicating @SQ line 8 | |
| duplicating @SQ line 9 | |
| duplicating @SQ line 10 | |
| duplicating @SQ line 11 | |
| duplicating @SQ line 12 | |
| duplicating @SQ line 13 | |
| duplicating @SQ line 14 | |
| duplicating @SQ line 15 | |
| duplicating @SQ line 16 | |
| duplicating @SQ line 17 | |
| duplicating @SQ line 18 | |
| duplicating @SQ line 19 | |
| duplicating @SQ line 20 | |
| duplicating @SQ line 21 | |
| duplicating @SQ line 22 | |
| duplicating @SQ line X | |
| duplicating @SQ line Y | |
| duplicating @SQ line MT | |
| duplicating @SQ line GL000207.1 | |
| duplicating @SQ line GL000226.1 | |
| duplicating @SQ line GL000229.1 | |
| duplicating @SQ line GL000231.1 | |
| duplicating @SQ line GL000210.1 | |
| duplicating @SQ line GL000239.1 | |
| duplicating @SQ line GL000235.1 | |
| duplicating @SQ line GL000201.1 | |
| duplicating @SQ line GL000247.1 | |
| duplicating @SQ line GL000245.1 | |
| duplicating @SQ line GL000197.1 | |
| duplicating @SQ line GL000203.1 | |
| duplicating @SQ line GL000246.1 | |
| duplicating @SQ line GL000249.1 | |
| duplicating @SQ line GL000196.1 | |
| duplicating @SQ line GL000248.1 | |
| duplicating @SQ line GL000244.1 | |
| duplicating @SQ line GL000238.1 | |
| duplicating @SQ line GL000202.1 | |
| duplicating @SQ line GL000234.1 | |
| duplicating @SQ line GL000232.1 | |
| duplicating @SQ line GL000206.1 | |
| duplicating @SQ line GL000240.1 | |
| duplicating @SQ line GL000236.1 | |
| duplicating @SQ line GL000241.1 | |
| duplicating @SQ line GL000243.1 | |
| duplicating @SQ line GL000242.1 | |
| duplicating @SQ line GL000230.1 | |
| duplicating @SQ line GL000237.1 | |
| duplicating @SQ line GL000233.1 | |
| duplicating @SQ line GL000204.1 | |
| duplicating @SQ line GL000198.1 | |
| duplicating @SQ line GL000208.1 | |
| duplicating @SQ line GL000191.1 | |
| duplicating @SQ line GL000227.1 | |
| duplicating @SQ line GL000228.1 | |
| duplicating @SQ line GL000214.1 | |
| duplicating @SQ line GL000221.1 | |
| duplicating @SQ line GL000209.1 | |
| duplicating @SQ line GL000218.1 | |
| duplicating @SQ line GL000220.1 | |
| duplicating @SQ line GL000213.1 | |
| duplicating @SQ line GL000211.1 | |
| duplicating @SQ line GL000199.1 | |
| duplicating @SQ line GL000217.1 | |
| duplicating @SQ line GL000216.1 | |
| duplicating @SQ line GL000215.1 | |
| duplicating @SQ line GL000205.1 | |
| duplicating @SQ line GL000219.1 | |
| duplicating @SQ line GL000224.1 | |
| duplicating @SQ line GL000223.1 | |
| duplicating @SQ line GL000195.1 | |
| duplicating @SQ line GL000212.1 | |
| duplicating @SQ line GL000222.1 | |
| duplicating @SQ line GL000200.1 | |
| duplicating @SQ line GL000193.1 | |
| duplicating @SQ line GL000194.1 | |
| duplicating @SQ line GL000225.1 | |
| duplicating @SQ line GL000192.1 | |
| ' returned non-zero exit status 1 | |
| cat: write error: Broken pipe | |
| 2016-07-28 00:24:24.822 [IPEngineApp] Exception in apply request: | |
| [0;31m[0m | |
| [0;31mCalledProcessError[0mTraceback (most recent call last) | |
| [0;32m<string>[0m in [0;36m<module>[0;34m()[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc[0m in [0;36m__call__[0;34m(self, *args, **kwargs)[0m | |
| [1;32m 71[0m [0;34m[0m[0m | |
| [1;32m 72[0m [0;32mdef[0m [0m__call__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m---> 73[0;31m [0;32mreturn[0m [0mself[0m[0;34m.[0m[0mf[0m[0;34m([0m[0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 74[0m [0;34m[0m[0m | |
| [1;32m 75[0m [0;32mif[0m [0;32mnot[0m [0mpy3compat[0m[0;34m.[0m[0mPY3[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc[0m in [0;36mprocess_alignment[0;34m(*args)[0m | |
| [1;32m 179[0m [0margs[0m [0;34m=[0m [0mipython[0m[0;34m.[0m[0munzip_args[0m[0;34m([0m[0margs[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 180[0m [0;32mwith[0m [0m_setup_logging[0m[0;34m([0m[0margs[0m[0;34m)[0m [0;32mas[0m [0mconfig[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m--> 181[0;31m [0;32mreturn[0m [0mipython[0m[0;34m.[0m[0mzip_args[0m[0;34m([0m[0mapply[0m[0;34m([0m[0msample[0m[0;34m.[0m[0mprocess_alignment[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 182[0m [0;34m[0m[0m | |
| [1;32m 183[0m [0;34m@[0m[0mrequire[0m[0;34m([0m[0malignprep[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc[0m in [0;36mprocess_alignment[0;34m(data, alt_input)[0m | |
| [1;32m 110[0m [0;32mif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0maligner[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 111[0m [0mlogger[0m[0;34m.[0m[0minfo[0m[0;34m([0m[0;34m"Aligning lane %s with %s aligner"[0m [0;34m%[0m [0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"rgnames"[0m[0;34m][0m[0;34m[[0m[0;34m"lane"[0m[0;34m][0m[0;34m,[0m [0maligner[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m--> 112[0;31m [0mdata[0m [0;34m=[0m [0malign_to_sort_bam[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0maligner[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 113[0m [0mdata[0m [0;34m=[0m [0m_add_supplemental_bams[0m[0;34m([0m[0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 114[0m [0;32melif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0mfastq1[0m[0;34m.[0m[0mendswith[0m[0;34m([0m[0;34m".bam"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36malign_to_sort_bam[0;34m(fastq1, fastq2, aligner, data)[0m | |
| [1;32m 62[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 63[0m data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file, | |
| [0;32m---> 64[0;31m names, align_dir, data) | |
| [0m[1;32m 65[0m [0;32mif[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;32mand[0m [0mutils[0m[0;34m.[0m[0mfile_exists[0m[0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 66[0m [0;32mif[0m [0;32mnot[0m [0mdata[0m[0;34m.[0m[0mget[0m[0;34m([0m[0;34m"align_split"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36m_align_from_fastq[0;34m(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)[0m | |
| [1;32m 115[0m [0mconfig[0m [0;34m=[0m [0mdata[0m[0;34m[[0m[0;34m"config"[0m[0;34m][0m[0;34m[0m[0m | |
| [1;32m 116[0m [0malign_fn[0m [0;34m=[0m [0mTOOLS[0m[0;34m[[0m[0maligner[0m[0;34m][0m[0;34m.[0m[0malign_fn[0m[0;34m[0m[0m | |
| [0;32m--> 117[0;31m [0mout[0m [0;34m=[0m [0malign_fn[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0malign_ref[0m[0;34m,[0m [0mnames[0m[0;34m,[0m [0malign_dir[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 118[0m [0;31m# handle align functions that update the main data dictionary in place[0m[0;34m[0m[0;34m[0m[0m | |
| [1;32m 119[0m [0;32mif[0m [0misinstance[0m[0;34m([0m[0mout[0m[0;34m,[0m [0mdict[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36malign_pipe[0;34m(fastq_file, pair_file, ref_file, names, align_dir, data)[0m | |
| [1;32m 145[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 146[0m out_file = _align_mem(fastq_file, pair_file, ref_file, out_file, | |
| [0;32m--> 147[0;31m names, rg_info, data) | |
| [0m[1;32m 148[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;34m=[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 149[0m [0;32mreturn[0m [0mdata[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36m_align_mem[0;34m(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)[0m | |
| [1;32m 155[0m [0mcmd[0m [0;34m=[0m [0;34m"%s | %s"[0m [0;34m%[0m [0;34m([0m[0m_get_bwa_mem_cmd[0m[0;34m([0m[0mdata[0m[0;34m,[0m [0mout_file[0m[0;34m,[0m [0mref_file[0m[0;34m,[0m [0mfastq_file[0m[0;34m,[0m [0mpair_file[0m[0;34m)[0m[0;34m,[0m [0mtobam_cl[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 156[0m do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None, | |
| [0;32m--> 157[0;31m [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)]) | |
| [0m[1;32m 158[0m [0;32mreturn[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 159[0m [0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36mrun[0;34m(cmd, descr, data, checks, region, log_error, log_stdout)[0m | |
| [1;32m 19[0m [0;32mtry[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 20[0m [0mlogger_cl[0m[0;34m.[0m[0mdebug[0m[0;34m([0m[0;34m" "[0m[0;34m.[0m[0mjoin[0m[0;34m([0m[0mstr[0m[0;34m([0m[0mx[0m[0;34m)[0m [0;32mfor[0m [0mx[0m [0;32min[0m [0mcmd[0m[0;34m)[0m [0;32mif[0m [0;32mnot[0m [0misinstance[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mbasestring[0m[0;34m)[0m [0;32melse[0m [0mcmd[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 21[0;31m [0m_do_run[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mchecks[0m[0;34m,[0m [0mlog_stdout[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 22[0m [0;32mexcept[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 23[0m [0mdiagnostics[0m[0;34m.[0m[0mend_cmd[0m[0;34m([0m[0mcmd_id[0m[0;34m,[0m [0mFalse[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36m_do_run[0;34m(cmd, checks, log_stdout)[0m | |
| [1;32m 93[0m [0ms[0m[0;34m.[0m[0mcommunicate[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 94[0m [0ms[0m[0;34m.[0m[0mstdout[0m[0;34m.[0m[0mclose[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 95[0;31m [0;32mraise[0m [0msubprocess[0m[0;34m.[0m[0mCalledProcessError[0m[0;34m([0m[0mexitcode[0m[0;34m,[0m [0merror_msg[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 96[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 97[0m [0;32mbreak[0m[0;34m[0m[0m | |
| [0;31mCalledProcessError[0m: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-1\tPL:illumina\tPU:NA12878-1\tSM:NA12878-1' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 20000001 40000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 20000001 40000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/af4269bd-f10e-4720-a1a0-d198e7dea2bb/tmpToEq1V/NA12878-1-sort-20000001_40000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/0b2a4e51-fdd7-486c-89f9-5e2106fb6b58/tmpeaxP4G/NA12878-1-sort-20000001_40000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/af4269bd-f10e-4720-a1a0-d198e7dea2bb/tmpToEq1V/NA12878-1-sort-20000001_40000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/0580ef0c-ae5e-4af2-a11e-6598a9b340c6/tmp_nXdx7/NA12878-1-sort-20000001_40000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/af4269bd-f10e-4720-a1a0-d198e7dea2bb/tmpToEq1V/NA12878-1-sort-20000001_40000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/af4269bd-f10e-4720-a1a0-d198e7dea2bb/tmpToEq1V/NA12878-1-sort-20000001_40000000.bam /dev/stdin | |
| samblaster: Version 0.1.22 | |
| samblaster: Inputting from stdin | |
| samblaster: Outputting to stdout | |
| samblaster: Opening /dev/fd/62 for write. | |
| samblaster: Opening /dev/fd/63 for write. | |
| [W::bseq_read] the 2nd file has fewer sequences. | |
| [M::mem_pestat] skip orientation FF as there are not enough pairs | |
| [M::mem_pestat] skip orientation FR as there are not enough pairs | |
| [M::mem_pestat] skip orientation RF as there are not enough pairs | |
| [M::mem_pestat] skip orientation RR as there are not enough pairs | |
| [mem_sam_pe] [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1106:12312:170243", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170" | |
| [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1106:12395:170197", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170" | |
| [mem_sam_pe] | |
| samblaster: Loaded 84 header sequence entries. | |
| ' returned non-zero exit status 1 | |
| cat: write error: Broken pipe | |
| 2016-07-28 00:25:16.471 [IPEngineApp] Exception in apply request: | |
| [0;31m[0m | |
| [0;31mCalledProcessError[0mTraceback (most recent call last) | |
| [0;32m<string>[0m in [0;36m<module>[0;34m()[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc[0m in [0;36m__call__[0;34m(self, *args, **kwargs)[0m | |
| [1;32m 71[0m [0;34m[0m[0m | |
| [1;32m 72[0m [0;32mdef[0m [0m__call__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m---> 73[0;31m [0;32mreturn[0m [0mself[0m[0;34m.[0m[0mf[0m[0;34m([0m[0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 74[0m [0;34m[0m[0m | |
| [1;32m 75[0m [0;32mif[0m [0;32mnot[0m [0mpy3compat[0m[0;34m.[0m[0mPY3[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc[0m in [0;36mprocess_alignment[0;34m(*args)[0m | |
| [1;32m 179[0m [0margs[0m [0;34m=[0m [0mipython[0m[0;34m.[0m[0munzip_args[0m[0;34m([0m[0margs[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 180[0m [0;32mwith[0m [0m_setup_logging[0m[0;34m([0m[0margs[0m[0;34m)[0m [0;32mas[0m [0mconfig[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m--> 181[0;31m [0;32mreturn[0m [0mipython[0m[0;34m.[0m[0mzip_args[0m[0;34m([0m[0mapply[0m[0;34m([0m[0msample[0m[0;34m.[0m[0mprocess_alignment[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 182[0m [0;34m[0m[0m | |
| [1;32m 183[0m [0;34m@[0m[0mrequire[0m[0;34m([0m[0malignprep[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc[0m in [0;36mprocess_alignment[0;34m(data, alt_input)[0m | |
| [1;32m 110[0m [0;32mif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0maligner[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 111[0m [0mlogger[0m[0;34m.[0m[0minfo[0m[0;34m([0m[0;34m"Aligning lane %s with %s aligner"[0m [0;34m%[0m [0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"rgnames"[0m[0;34m][0m[0;34m[[0m[0;34m"lane"[0m[0;34m][0m[0;34m,[0m [0maligner[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m--> 112[0;31m [0mdata[0m [0;34m=[0m [0malign_to_sort_bam[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0maligner[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 113[0m [0mdata[0m [0;34m=[0m [0m_add_supplemental_bams[0m[0;34m([0m[0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 114[0m [0;32melif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0mfastq1[0m[0;34m.[0m[0mendswith[0m[0;34m([0m[0;34m".bam"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36malign_to_sort_bam[0;34m(fastq1, fastq2, aligner, data)[0m | |
| [1;32m 62[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 63[0m data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file, | |
| [0;32m---> 64[0;31m names, align_dir, data) | |
| [0m[1;32m 65[0m [0;32mif[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;32mand[0m [0mutils[0m[0;34m.[0m[0mfile_exists[0m[0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 66[0m [0;32mif[0m [0;32mnot[0m [0mdata[0m[0;34m.[0m[0mget[0m[0;34m([0m[0;34m"align_split"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36m_align_from_fastq[0;34m(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)[0m | |
| [1;32m 115[0m [0mconfig[0m [0;34m=[0m [0mdata[0m[0;34m[[0m[0;34m"config"[0m[0;34m][0m[0;34m[0m[0m | |
| [1;32m 116[0m [0malign_fn[0m [0;34m=[0m [0mTOOLS[0m[0;34m[[0m[0maligner[0m[0;34m][0m[0;34m.[0m[0malign_fn[0m[0;34m[0m[0m | |
| [0;32m--> 117[0;31m [0mout[0m [0;34m=[0m [0malign_fn[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0malign_ref[0m[0;34m,[0m [0mnames[0m[0;34m,[0m [0malign_dir[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 118[0m [0;31m# handle align functions that update the main data dictionary in place[0m[0;34m[0m[0;34m[0m[0m | |
| [1;32m 119[0m [0;32mif[0m [0misinstance[0m[0;34m([0m[0mout[0m[0;34m,[0m [0mdict[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36malign_pipe[0;34m(fastq_file, pair_file, ref_file, names, align_dir, data)[0m | |
| [1;32m 145[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 146[0m out_file = _align_mem(fastq_file, pair_file, ref_file, out_file, | |
| [0;32m--> 147[0;31m names, rg_info, data) | |
| [0m[1;32m 148[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;34m=[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 149[0m [0;32mreturn[0m [0mdata[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36m_align_mem[0;34m(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)[0m | |
| [1;32m 155[0m [0mcmd[0m [0;34m=[0m [0;34m"%s | %s"[0m [0;34m%[0m [0;34m([0m[0m_get_bwa_mem_cmd[0m[0;34m([0m[0mdata[0m[0;34m,[0m [0mout_file[0m[0;34m,[0m [0mref_file[0m[0;34m,[0m [0mfastq_file[0m[0;34m,[0m [0mpair_file[0m[0;34m)[0m[0;34m,[0m [0mtobam_cl[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 156[0m do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None, | |
| [0;32m--> 157[0;31m [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)]) | |
| [0m[1;32m 158[0m [0;32mreturn[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 159[0m [0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36mrun[0;34m(cmd, descr, data, checks, region, log_error, log_stdout)[0m | |
| [1;32m 19[0m [0;32mtry[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 20[0m [0mlogger_cl[0m[0;34m.[0m[0mdebug[0m[0;34m([0m[0;34m" "[0m[0;34m.[0m[0mjoin[0m[0;34m([0m[0mstr[0m[0;34m([0m[0mx[0m[0;34m)[0m [0;32mfor[0m [0mx[0m [0;32min[0m [0mcmd[0m[0;34m)[0m [0;32mif[0m [0;32mnot[0m [0misinstance[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mbasestring[0m[0;34m)[0m [0;32melse[0m [0mcmd[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 21[0;31m [0m_do_run[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mchecks[0m[0;34m,[0m [0mlog_stdout[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 22[0m [0;32mexcept[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 23[0m [0mdiagnostics[0m[0;34m.[0m[0mend_cmd[0m[0;34m([0m[0mcmd_id[0m[0;34m,[0m [0mFalse[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36m_do_run[0;34m(cmd, checks, log_stdout)[0m | |
| [1;32m 93[0m [0ms[0m[0;34m.[0m[0mcommunicate[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 94[0m [0ms[0m[0;34m.[0m[0mstdout[0m[0;34m.[0m[0mclose[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 95[0;31m [0;32mraise[0m [0msubprocess[0m[0;34m.[0m[0mCalledProcessError[0m[0;34m([0m[0mexitcode[0m[0;34m,[0m [0merror_msg[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 96[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 97[0m [0;32mbreak[0m[0;34m[0m[0m | |
| [0;31mCalledProcessError[0m: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-1\tPL:illumina\tPU:NA12878-1\tSM:NA12878-1' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 140000001 160000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 140000001 160000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/50889a34-56fb-4439-9ef7-4c2e669abbe9/tmpbPyql6/NA12878-1-sort-140000001_160000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/11059b50-cc75-445d-af19-cab36c0ac036/tmp4_21V4/NA12878-1-sort-140000001_160000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/50889a34-56fb-4439-9ef7-4c2e669abbe9/tmpbPyql6/NA12878-1-sort-140000001_160000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/70a00351-292c-4622-96c5-0d39f7564844/tmpxIdHOp/NA12878-1-sort-140000001_160000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/50889a34-56fb-4439-9ef7-4c2e669abbe9/tmpbPyql6/NA12878-1-sort-140000001_160000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/50889a34-56fb-4439-9ef7-4c2e669abbe9/tmpbPyql6/NA12878-1-sort-140000001_160000000.bam /dev/stdin | |
| duplicating @SQ line GL000199.1 | |
| duplicating @SQ line GL000217.1 | |
| duplicating @SQ line GL000216.1 | |
| duplicating @SQ line GL000215.1 | |
| duplicating @SQ line GL000205.1 | |
| duplicating @SQ line GL000219.1 | |
| duplicating @SQ line GL000224.1 | |
| duplicating @SQ line GL000223.1 | |
| duplicating @SQ line GL000195.1 | |
| duplicating @SQ line GL000212.1 | |
| duplicating @SQ line GL000222.1 | |
| duplicating @SQ line GL000200.1 | |
| duplicating @SQ line GL000193.1 | |
| duplicating @SQ line GL000194.1 | |
| duplicating @SQ line GL000225.1 | |
| duplicating @SQ line GL000192.1 | |
| duplicating @SQ line 1 | |
| duplicating @SQ line 2 | |
| duplicating @SQ line 3 | |
| duplicating @SQ line 4 | |
| duplicating @SQ line 5 | |
| duplicating @SQ line 6 | |
| duplicating @SQ line 7 | |
| duplicating @SQ line 8 | |
| duplicating @SQ line 9 | |
| duplicating @SQ line 10 | |
| duplicating @SQ line 11 | |
| duplicating @SQ line 12 | |
| duplicating @SQ line 13 | |
| duplicating @SQ line 14 | |
| duplicating @SQ line 15 | |
| duplicating @SQ line 16 | |
| duplicating @SQ line 17 | |
| duplicating @SQ line 18 | |
| duplicating @SQ line 19 | |
| duplicating @SQ line 20 | |
| duplicating @SQ line 21 | |
| duplicating @SQ line 22 | |
| duplicating @SQ line X | |
| duplicating @SQ line Y | |
| duplicating @SQ line MT | |
| duplicating @SQ line GL000207.1 | |
| duplicating @SQ line GL000226.1 | |
| duplicating @SQ line GL000229.1 | |
| duplicating @SQ line GL000231.1 | |
| duplicating @SQ line GL000210.1 | |
| duplicating @SQ line GL000239.1 | |
| duplicating @SQ line GL000235.1 | |
| duplicating @SQ line GL000201.1 | |
| duplicating @SQ line GL000247.1 | |
| duplicating @SQ line GL000245.1 | |
| duplicating @SQ line GL000197.1 | |
| duplicating @SQ line GL000203.1 | |
| duplicating @SQ line GL000246.1 | |
| duplicating @SQ line GL000249.1 | |
| duplicating @SQ line GL000196.1 | |
| duplicating @SQ line GL000248.1 | |
| duplicating @SQ line GL000244.1 | |
| duplicating @SQ line GL000238.1 | |
| duplicating @SQ line GL000202.1 | |
| duplicating @SQ line GL000234.1 | |
| duplicating @SQ line GL000232.1 | |
| duplicating @SQ line GL000206.1 | |
| duplicating @SQ line GL000240.1 | |
| duplicating @SQ line GL000236.1 | |
| duplicating @SQ line GL000241.1 | |
| duplicating @SQ line GL000243.1 | |
| duplicating @SQ line GL000242.1 | |
| duplicating @SQ line GL000230.1 | |
| duplicating @SQ line GL000237.1 | |
| duplicating @SQ line GL000233.1 | |
| duplicating @SQ line GL000204.1 | |
| duplicating @SQ line GL000198.1 | |
| duplicating @SQ line GL000208.1 | |
| duplicating @SQ line GL000191.1 | |
| duplicating @SQ line GL000227.1 | |
| duplicating @SQ line GL000228.1 | |
| duplicating @SQ line GL000214.1 | |
| duplicating @SQ line GL000221.1 | |
| duplicating @SQ line GL000209.1 | |
| duplicating @SQ line GL000218.1 | |
| duplicating @SQ line GL000220.1 | |
| duplicating @SQ line GL000213.1 | |
| duplicating @SQ line GL000211.1 | |
| duplicating @SQ line GL000199.1 | |
| duplicating @SQ line GL000217.1 | |
| duplicating @SQ line GL000216.1 | |
| duplicating @SQ line GL000215.1 | |
| duplicating @SQ line GL000205.1 | |
| duplicating @SQ line GL000219.1 | |
| duplicating @SQ line GL000224.1 | |
| duplicating @SQ line GL000223.1 | |
| duplicating @SQ line GL000195.1 | |
| duplicating @SQ line GL000212.1 | |
| duplicating @SQ line GL000222.1 | |
| duplicating @SQ line GL000200.1 | |
| duplicating @SQ line GL000193.1 | |
| duplicating @SQ line GL000194.1 | |
| duplicating @SQ line GL000225.1 | |
| duplicating @SQ line GL000192.1 | |
| ' returned non-zero exit status 1 | |
| cat: write error: Broken pipe | |
| 2016-07-28 00:25:39.162 [IPEngineApp] Exception in apply request: | |
| [0;31m[0m | |
| [0;31mCalledProcessError[0mTraceback (most recent call last) | |
| [0;32m<string>[0m in [0;36m<module>[0;34m()[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc[0m in [0;36m__call__[0;34m(self, *args, **kwargs)[0m | |
| [1;32m 71[0m [0;34m[0m[0m | |
| [1;32m 72[0m [0;32mdef[0m [0m__call__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m---> 73[0;31m [0;32mreturn[0m [0mself[0m[0;34m.[0m[0mf[0m[0;34m([0m[0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 74[0m [0;34m[0m[0m | |
| [1;32m 75[0m [0;32mif[0m [0;32mnot[0m [0mpy3compat[0m[0;34m.[0m[0mPY3[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc[0m in [0;36mprocess_alignment[0;34m(*args)[0m | |
| [1;32m 179[0m [0margs[0m [0;34m=[0m [0mipython[0m[0;34m.[0m[0munzip_args[0m[0;34m([0m[0margs[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 180[0m [0;32mwith[0m [0m_setup_logging[0m[0;34m([0m[0margs[0m[0;34m)[0m [0;32mas[0m [0mconfig[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m--> 181[0;31m [0;32mreturn[0m [0mipython[0m[0;34m.[0m[0mzip_args[0m[0;34m([0m[0mapply[0m[0;34m([0m[0msample[0m[0;34m.[0m[0mprocess_alignment[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 182[0m [0;34m[0m[0m | |
| [1;32m 183[0m [0;34m@[0m[0mrequire[0m[0;34m([0m[0malignprep[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc[0m in [0;36mprocess_alignment[0;34m(data, alt_input)[0m | |
| [1;32m 110[0m [0;32mif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0maligner[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 111[0m [0mlogger[0m[0;34m.[0m[0minfo[0m[0;34m([0m[0;34m"Aligning lane %s with %s aligner"[0m [0;34m%[0m [0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"rgnames"[0m[0;34m][0m[0;34m[[0m[0;34m"lane"[0m[0;34m][0m[0;34m,[0m [0maligner[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m--> 112[0;31m [0mdata[0m [0;34m=[0m [0malign_to_sort_bam[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0maligner[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 113[0m [0mdata[0m [0;34m=[0m [0m_add_supplemental_bams[0m[0;34m([0m[0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 114[0m [0;32melif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0mfastq1[0m[0;34m.[0m[0mendswith[0m[0;34m([0m[0;34m".bam"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36malign_to_sort_bam[0;34m(fastq1, fastq2, aligner, data)[0m | |
| [1;32m 62[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 63[0m data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file, | |
| [0;32m---> 64[0;31m names, align_dir, data) | |
| [0m[1;32m 65[0m [0;32mif[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;32mand[0m [0mutils[0m[0;34m.[0m[0mfile_exists[0m[0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 66[0m [0;32mif[0m [0;32mnot[0m [0mdata[0m[0;34m.[0m[0mget[0m[0;34m([0m[0;34m"align_split"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36m_align_from_fastq[0;34m(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)[0m | |
| [1;32m 115[0m [0mconfig[0m [0;34m=[0m [0mdata[0m[0;34m[[0m[0;34m"config"[0m[0;34m][0m[0;34m[0m[0m | |
| [1;32m 116[0m [0malign_fn[0m [0;34m=[0m [0mTOOLS[0m[0;34m[[0m[0maligner[0m[0;34m][0m[0;34m.[0m[0malign_fn[0m[0;34m[0m[0m | |
| [0;32m--> 117[0;31m [0mout[0m [0;34m=[0m [0malign_fn[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0malign_ref[0m[0;34m,[0m [0mnames[0m[0;34m,[0m [0malign_dir[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 118[0m [0;31m# handle align functions that update the main data dictionary in place[0m[0;34m[0m[0;34m[0m[0m | |
| [1;32m 119[0m [0;32mif[0m [0misinstance[0m[0;34m([0m[0mout[0m[0;34m,[0m [0mdict[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36malign_pipe[0;34m(fastq_file, pair_file, ref_file, names, align_dir, data)[0m | |
| [1;32m 145[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 146[0m out_file = _align_mem(fastq_file, pair_file, ref_file, out_file, | |
| [0;32m--> 147[0;31m names, rg_info, data) | |
| [0m[1;32m 148[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;34m=[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 149[0m [0;32mreturn[0m [0mdata[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36m_align_mem[0;34m(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)[0m | |
| [1;32m 155[0m [0mcmd[0m [0;34m=[0m [0;34m"%s | %s"[0m [0;34m%[0m [0;34m([0m[0m_get_bwa_mem_cmd[0m[0;34m([0m[0mdata[0m[0;34m,[0m [0mout_file[0m[0;34m,[0m [0mref_file[0m[0;34m,[0m [0mfastq_file[0m[0;34m,[0m [0mpair_file[0m[0;34m)[0m[0;34m,[0m [0mtobam_cl[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 156[0m do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None, | |
| [0;32m--> 157[0;31m [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)]) | |
| [0m[1;32m 158[0m [0;32mreturn[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 159[0m [0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36mrun[0;34m(cmd, descr, data, checks, region, log_error, log_stdout)[0m | |
| [1;32m 19[0m [0;32mtry[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 20[0m [0mlogger_cl[0m[0;34m.[0m[0mdebug[0m[0;34m([0m[0;34m" "[0m[0;34m.[0m[0mjoin[0m[0;34m([0m[0mstr[0m[0;34m([0m[0mx[0m[0;34m)[0m [0;32mfor[0m [0mx[0m [0;32min[0m [0mcmd[0m[0;34m)[0m [0;32mif[0m [0;32mnot[0m [0misinstance[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mbasestring[0m[0;34m)[0m [0;32melse[0m [0mcmd[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 21[0;31m [0m_do_run[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mchecks[0m[0;34m,[0m [0mlog_stdout[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 22[0m [0;32mexcept[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 23[0m [0mdiagnostics[0m[0;34m.[0m[0mend_cmd[0m[0;34m([0m[0mcmd_id[0m[0;34m,[0m [0mFalse[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36m_do_run[0;34m(cmd, checks, log_stdout)[0m | |
| [1;32m 93[0m [0ms[0m[0;34m.[0m[0mcommunicate[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 94[0m [0ms[0m[0;34m.[0m[0mstdout[0m[0;34m.[0m[0mclose[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 95[0;31m [0;32mraise[0m [0msubprocess[0m[0;34m.[0m[0mCalledProcessError[0m[0;34m([0m[0mexitcode[0m[0;34m,[0m [0merror_msg[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 96[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 97[0m [0;32mbreak[0m[0;34m[0m[0m | |
| [0;31mCalledProcessError[0m: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-1\tPL:illumina\tPU:NA12878-1\tSM:NA12878-1' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 40000001 60000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 40000001 60000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/795eca19-e8ea-4975-b3f1-dfa313fa510d/tmp4q7JE4/NA12878-1-sort-40000001_60000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/0c640066-4500-4885-9b67-054cbc2a43f1/tmpab_NFG/NA12878-1-sort-40000001_60000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/795eca19-e8ea-4975-b3f1-dfa313fa510d/tmp4q7JE4/NA12878-1-sort-40000001_60000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/b9e37910-f953-4684-b5cc-fc55b99b5b6f/tmpQouZrN/NA12878-1-sort-40000001_60000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/795eca19-e8ea-4975-b3f1-dfa313fa510d/tmp4q7JE4/NA12878-1-sort-40000001_60000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/795eca19-e8ea-4975-b3f1-dfa313fa510d/tmp4q7JE4/NA12878-1-sort-40000001_60000000.bam /dev/stdin | |
| [W::sam_hdr_parse] duplicated sequence 'GL000216.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000215.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000205.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000219.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000224.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000223.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000195.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000212.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000222.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000200.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000193.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000194.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000225.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000192.1' | |
| duplicating @RG line NA12878-1 | |
| duplicating @PG line bwa | |
| duplicating @SQ line 1 | |
| duplicating @SQ line 2 | |
| duplicating @SQ line 3 | |
| duplicating @SQ line 4 | |
| duplicating @SQ line 5 | |
| duplicating @SQ line 6 | |
| duplicating @SQ line 7 | |
| duplicating @SQ line 8 | |
| duplicating @SQ line 9 | |
| duplicating @SQ line 10 | |
| duplicating @SQ line 11 | |
| duplicating @SQ line 12 | |
| duplicating @SQ line 13 | |
| duplicating @SQ line 14 | |
| duplicating @SQ line 15 | |
| duplicating @SQ line 16 | |
| duplicating @SQ line 17 | |
| duplicating @SQ line 18 | |
| duplicating @SQ line 19 | |
| duplicating @SQ line 20 | |
| duplicating @SQ line 21 | |
| duplicating @SQ line 22 | |
| duplicating @SQ line X | |
| duplicating @SQ line Y | |
| duplicating @SQ line MT | |
| duplicating @SQ line GL000207.1 | |
| duplicating @SQ line GL000226.1 | |
| duplicating @SQ line GL000229.1 | |
| duplicating @SQ line GL000231.1 | |
| duplicating @SQ line GL000210.1 | |
| duplicating @SQ line GL000239.1 | |
| duplicating @SQ line GL000235.1 | |
| duplicating @SQ line GL000201.1 | |
| duplicating @SQ line GL000247.1 | |
| duplicating @SQ line GL000245.1 | |
| duplicating @SQ line GL000197.1 | |
| duplicating @SQ line GL000203.1 | |
| duplicating @SQ line GL000246.1 | |
| duplicating @SQ line GL000249.1 | |
| duplicating @SQ line GL000196.1 | |
| duplicating @SQ line GL000248.1 | |
| duplicating @SQ line GL000244.1 | |
| duplicating @SQ line GL000238.1 | |
| duplicating @SQ line GL000202.1 | |
| duplicating @SQ line GL000234.1 | |
| duplicating @SQ line GL000232.1 | |
| duplicating @SQ line GL000206.1 | |
| duplicating @SQ line GL000240.1 | |
| duplicating @SQ line GL000236.1 | |
| duplicating @SQ line GL000241.1 | |
| duplicating @SQ line GL000243.1 | |
| duplicating @SQ line GL000242.1 | |
| duplicating @SQ line GL000230.1 | |
| duplicating @SQ line GL000237.1 | |
| duplicating @SQ line GL000233.1 | |
| duplicating @SQ line GL000204.1 | |
| duplicating @SQ line GL000198.1 | |
| duplicating @SQ line GL000208.1 | |
| duplicating @SQ line GL000191.1 | |
| duplicating @SQ line GL000227.1 | |
| duplicating @SQ line GL000228.1 | |
| duplicating @SQ line GL000214.1 | |
| duplicating @SQ line GL000221.1 | |
| duplicating @SQ line GL000209.1 | |
| duplicating @SQ line GL000218.1 | |
| duplicating @SQ line GL000220.1 | |
| duplicating @SQ line GL000213.1 | |
| duplicating @SQ line GL000211.1 | |
| duplicating @SQ line GL000199.1 | |
| duplicating @SQ line GL000217.1 | |
| duplicating @SQ line GL000216.1 | |
| duplicating @SQ line GL000215.1 | |
| duplicating @SQ line GL000205.1 | |
| duplicating @SQ line GL000219.1 | |
| duplicating @SQ line GL000224.1 | |
| duplicating @SQ line GL000223.1 | |
| duplicating @SQ line GL000195.1 | |
| duplicating @SQ line GL000212.1 | |
| duplicating @SQ line GL000222.1 | |
| duplicating @SQ line GL000200.1 | |
| duplicating @SQ line GL000193.1 | |
| duplicating @SQ line GL000194.1 | |
| duplicating @SQ line GL000225.1 | |
| duplicating @SQ line GL000192.1 | |
| ' returned non-zero exit status 1 | |
| cat: write error: Broken pipe | |
| 2016-07-28 00:26:30.179 [IPEngineApp] Exception in apply request: | |
| [0;31m[0m | |
| [0;31mCalledProcessError[0mTraceback (most recent call last) | |
| [0;32m<string>[0m in [0;36m<module>[0;34m()[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc[0m in [0;36m__call__[0;34m(self, *args, **kwargs)[0m | |
| [1;32m 71[0m [0;34m[0m[0m | |
| [1;32m 72[0m [0;32mdef[0m [0m__call__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m---> 73[0;31m [0;32mreturn[0m [0mself[0m[0;34m.[0m[0mf[0m[0;34m([0m[0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 74[0m [0;34m[0m[0m | |
| [1;32m 75[0m [0;32mif[0m [0;32mnot[0m [0mpy3compat[0m[0;34m.[0m[0mPY3[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc[0m in [0;36mprocess_alignment[0;34m(*args)[0m | |
| [1;32m 179[0m [0margs[0m [0;34m=[0m [0mipython[0m[0;34m.[0m[0munzip_args[0m[0;34m([0m[0margs[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 180[0m [0;32mwith[0m [0m_setup_logging[0m[0;34m([0m[0margs[0m[0;34m)[0m [0;32mas[0m [0mconfig[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m--> 181[0;31m [0;32mreturn[0m [0mipython[0m[0;34m.[0m[0mzip_args[0m[0;34m([0m[0mapply[0m[0;34m([0m[0msample[0m[0;34m.[0m[0mprocess_alignment[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 182[0m [0;34m[0m[0m | |
| [1;32m 183[0m [0;34m@[0m[0mrequire[0m[0;34m([0m[0malignprep[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc[0m in [0;36mprocess_alignment[0;34m(data, alt_input)[0m | |
| [1;32m 110[0m [0;32mif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0maligner[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 111[0m [0mlogger[0m[0;34m.[0m[0minfo[0m[0;34m([0m[0;34m"Aligning lane %s with %s aligner"[0m [0;34m%[0m [0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"rgnames"[0m[0;34m][0m[0;34m[[0m[0;34m"lane"[0m[0;34m][0m[0;34m,[0m [0maligner[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m--> 112[0;31m [0mdata[0m [0;34m=[0m [0malign_to_sort_bam[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0maligner[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 113[0m [0mdata[0m [0;34m=[0m [0m_add_supplemental_bams[0m[0;34m([0m[0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 114[0m [0;32melif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0mfastq1[0m[0;34m.[0m[0mendswith[0m[0;34m([0m[0;34m".bam"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36malign_to_sort_bam[0;34m(fastq1, fastq2, aligner, data)[0m | |
| [1;32m 62[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 63[0m data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file, | |
| [0;32m---> 64[0;31m names, align_dir, data) | |
| [0m[1;32m 65[0m [0;32mif[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;32mand[0m [0mutils[0m[0;34m.[0m[0mfile_exists[0m[0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 66[0m [0;32mif[0m [0;32mnot[0m [0mdata[0m[0;34m.[0m[0mget[0m[0;34m([0m[0;34m"align_split"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36m_align_from_fastq[0;34m(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)[0m | |
| [1;32m 115[0m [0mconfig[0m [0;34m=[0m [0mdata[0m[0;34m[[0m[0;34m"config"[0m[0;34m][0m[0;34m[0m[0m | |
| [1;32m 116[0m [0malign_fn[0m [0;34m=[0m [0mTOOLS[0m[0;34m[[0m[0maligner[0m[0;34m][0m[0;34m.[0m[0malign_fn[0m[0;34m[0m[0m | |
| [0;32m--> 117[0;31m [0mout[0m [0;34m=[0m [0malign_fn[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0malign_ref[0m[0;34m,[0m [0mnames[0m[0;34m,[0m [0malign_dir[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 118[0m [0;31m# handle align functions that update the main data dictionary in place[0m[0;34m[0m[0;34m[0m[0m | |
| [1;32m 119[0m [0;32mif[0m [0misinstance[0m[0;34m([0m[0mout[0m[0;34m,[0m [0mdict[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36malign_pipe[0;34m(fastq_file, pair_file, ref_file, names, align_dir, data)[0m | |
| [1;32m 145[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 146[0m out_file = _align_mem(fastq_file, pair_file, ref_file, out_file, | |
| [0;32m--> 147[0;31m names, rg_info, data) | |
| [0m[1;32m 148[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;34m=[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 149[0m [0;32mreturn[0m [0mdata[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36m_align_mem[0;34m(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)[0m | |
| [1;32m 155[0m [0mcmd[0m [0;34m=[0m [0;34m"%s | %s"[0m [0;34m%[0m [0;34m([0m[0m_get_bwa_mem_cmd[0m[0;34m([0m[0mdata[0m[0;34m,[0m [0mout_file[0m[0;34m,[0m [0mref_file[0m[0;34m,[0m [0mfastq_file[0m[0;34m,[0m [0mpair_file[0m[0;34m)[0m[0;34m,[0m [0mtobam_cl[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 156[0m do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None, | |
| [0;32m--> 157[0;31m [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)]) | |
| [0m[1;32m 158[0m [0;32mreturn[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 159[0m [0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36mrun[0;34m(cmd, descr, data, checks, region, log_error, log_stdout)[0m | |
| [1;32m 19[0m [0;32mtry[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 20[0m [0mlogger_cl[0m[0;34m.[0m[0mdebug[0m[0;34m([0m[0;34m" "[0m[0;34m.[0m[0mjoin[0m[0;34m([0m[0mstr[0m[0;34m([0m[0mx[0m[0;34m)[0m [0;32mfor[0m [0mx[0m [0;32min[0m [0mcmd[0m[0;34m)[0m [0;32mif[0m [0;32mnot[0m [0misinstance[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mbasestring[0m[0;34m)[0m [0;32melse[0m [0mcmd[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 21[0;31m [0m_do_run[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mchecks[0m[0;34m,[0m [0mlog_stdout[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 22[0m [0;32mexcept[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 23[0m [0mdiagnostics[0m[0;34m.[0m[0mend_cmd[0m[0;34m([0m[0mcmd_id[0m[0;34m,[0m [0mFalse[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36m_do_run[0;34m(cmd, checks, log_stdout)[0m | |
| [1;32m 93[0m [0ms[0m[0;34m.[0m[0mcommunicate[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 94[0m [0ms[0m[0;34m.[0m[0mstdout[0m[0;34m.[0m[0mclose[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 95[0;31m [0;32mraise[0m [0msubprocess[0m[0;34m.[0m[0mCalledProcessError[0m[0;34m([0m[0mexitcode[0m[0;34m,[0m [0merror_msg[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 96[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 97[0m [0;32mbreak[0m[0;34m[0m[0m | |
| [0;31mCalledProcessError[0m: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-1\tPL:illumina\tPU:NA12878-1\tSM:NA12878-1' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 120000001 140000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 120000001 140000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/8bb544a1-303b-455b-9ebf-63c52f86c6af/tmpKHmrws/NA12878-1-sort-120000001_140000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/f14153ed-58d9-4a5a-9ed6-d1f02a521533/tmpOXeBPn/NA12878-1-sort-120000001_140000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/8bb544a1-303b-455b-9ebf-63c52f86c6af/tmpKHmrws/NA12878-1-sort-120000001_140000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/0e4f2576-aa97-4404-9f84-2c9f77b1e7f3/tmpzy52Mp/NA12878-1-sort-120000001_140000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/8bb544a1-303b-455b-9ebf-63c52f86c6af/tmpKHmrws/NA12878-1-sort-120000001_140000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/8bb544a1-303b-455b-9ebf-63c52f86c6af/tmpKHmrws/NA12878-1-sort-120000001_140000000.bam /dev/stdin | |
| samblaster: Version 0.1.22 | |
| samblaster: Inputting from stdin | |
| samblaster: Outputting to stdout | |
| samblaster: Opening /dev/fd/62 for write. | |
| samblaster: Opening /dev/fd/63 for write. | |
| [M::mem_pestat] skip orientation FF as there are not enough pairs | |
| [M::mem_pestat] skip orientation FR as there are not enough pairs | |
| [M::mem_pestat] skip orientation RF as there are not enough pairs | |
| [M::mem_pestat] skip orientation RR as there are not enough pairs | |
| [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:2201:20705:113542", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170" | |
| [mem_sam_pe] [mem_sam_pe] [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:2201:20606:113544", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170" | |
| [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:2201:21059:113535", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170" | |
| [mem_sam_pe] samblaster: Loaded 84 header sequence entries. | |
| ' returned non-zero exit status 1 | |
| cat: write error: Broken pipe | |
| 2016-07-28 00:27:20.810 [IPEngineApp] Exception in apply request: | |
| [0;31m[0m | |
| [0;31mCalledProcessError[0mTraceback (most recent call last) | |
| [0;32m<string>[0m in [0;36m<module>[0;34m()[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc[0m in [0;36m__call__[0;34m(self, *args, **kwargs)[0m | |
| [1;32m 71[0m [0;34m[0m[0m | |
| [1;32m 72[0m [0;32mdef[0m [0m__call__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m---> 73[0;31m [0;32mreturn[0m [0mself[0m[0;34m.[0m[0mf[0m[0;34m([0m[0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 74[0m [0;34m[0m[0m | |
| [1;32m 75[0m [0;32mif[0m [0;32mnot[0m [0mpy3compat[0m[0;34m.[0m[0mPY3[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc[0m in [0;36mprocess_alignment[0;34m(*args)[0m | |
| [1;32m 179[0m [0margs[0m [0;34m=[0m [0mipython[0m[0;34m.[0m[0munzip_args[0m[0;34m([0m[0margs[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 180[0m [0;32mwith[0m [0m_setup_logging[0m[0;34m([0m[0margs[0m[0;34m)[0m [0;32mas[0m [0mconfig[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m--> 181[0;31m [0;32mreturn[0m [0mipython[0m[0;34m.[0m[0mzip_args[0m[0;34m([0m[0mapply[0m[0;34m([0m[0msample[0m[0;34m.[0m[0mprocess_alignment[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 182[0m [0;34m[0m[0m | |
| [1;32m 183[0m [0;34m@[0m[0mrequire[0m[0;34m([0m[0malignprep[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc[0m in [0;36mprocess_alignment[0;34m(data, alt_input)[0m | |
| [1;32m 110[0m [0;32mif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0maligner[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 111[0m [0mlogger[0m[0;34m.[0m[0minfo[0m[0;34m([0m[0;34m"Aligning lane %s with %s aligner"[0m [0;34m%[0m [0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"rgnames"[0m[0;34m][0m[0;34m[[0m[0;34m"lane"[0m[0;34m][0m[0;34m,[0m [0maligner[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m--> 112[0;31m [0mdata[0m [0;34m=[0m [0malign_to_sort_bam[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0maligner[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 113[0m [0mdata[0m [0;34m=[0m [0m_add_supplemental_bams[0m[0;34m([0m[0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 114[0m [0;32melif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0mfastq1[0m[0;34m.[0m[0mendswith[0m[0;34m([0m[0;34m".bam"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36malign_to_sort_bam[0;34m(fastq1, fastq2, aligner, data)[0m | |
| [1;32m 62[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 63[0m data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file, | |
| [0;32m---> 64[0;31m names, align_dir, data) | |
| [0m[1;32m 65[0m [0;32mif[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;32mand[0m [0mutils[0m[0;34m.[0m[0mfile_exists[0m[0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 66[0m [0;32mif[0m [0;32mnot[0m [0mdata[0m[0;34m.[0m[0mget[0m[0;34m([0m[0;34m"align_split"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36m_align_from_fastq[0;34m(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)[0m | |
| [1;32m 115[0m [0mconfig[0m [0;34m=[0m [0mdata[0m[0;34m[[0m[0;34m"config"[0m[0;34m][0m[0;34m[0m[0m | |
| [1;32m 116[0m [0malign_fn[0m [0;34m=[0m [0mTOOLS[0m[0;34m[[0m[0maligner[0m[0;34m][0m[0;34m.[0m[0malign_fn[0m[0;34m[0m[0m | |
| [0;32m--> 117[0;31m [0mout[0m [0;34m=[0m [0malign_fn[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0malign_ref[0m[0;34m,[0m [0mnames[0m[0;34m,[0m [0malign_dir[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 118[0m [0;31m# handle align functions that update the main data dictionary in place[0m[0;34m[0m[0;34m[0m[0m | |
| [1;32m 119[0m [0;32mif[0m [0misinstance[0m[0;34m([0m[0mout[0m[0;34m,[0m [0mdict[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36malign_pipe[0;34m(fastq_file, pair_file, ref_file, names, align_dir, data)[0m | |
| [1;32m 145[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 146[0m out_file = _align_mem(fastq_file, pair_file, ref_file, out_file, | |
| [0;32m--> 147[0;31m names, rg_info, data) | |
| [0m[1;32m 148[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;34m=[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 149[0m [0;32mreturn[0m [0mdata[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36m_align_mem[0;34m(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)[0m | |
| [1;32m 155[0m [0mcmd[0m [0;34m=[0m [0;34m"%s | %s"[0m [0;34m%[0m [0;34m([0m[0m_get_bwa_mem_cmd[0m[0;34m([0m[0mdata[0m[0;34m,[0m [0mout_file[0m[0;34m,[0m [0mref_file[0m[0;34m,[0m [0mfastq_file[0m[0;34m,[0m [0mpair_file[0m[0;34m)[0m[0;34m,[0m [0mtobam_cl[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 156[0m do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None, | |
| [0;32m--> 157[0;31m [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)]) | |
| [0m[1;32m 158[0m [0;32mreturn[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 159[0m [0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36mrun[0;34m(cmd, descr, data, checks, region, log_error, log_stdout)[0m | |
| [1;32m 19[0m [0;32mtry[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 20[0m [0mlogger_cl[0m[0;34m.[0m[0mdebug[0m[0;34m([0m[0;34m" "[0m[0;34m.[0m[0mjoin[0m[0;34m([0m[0mstr[0m[0;34m([0m[0mx[0m[0;34m)[0m [0;32mfor[0m [0mx[0m [0;32min[0m [0mcmd[0m[0;34m)[0m [0;32mif[0m [0;32mnot[0m [0misinstance[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mbasestring[0m[0;34m)[0m [0;32melse[0m [0mcmd[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 21[0;31m [0m_do_run[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mchecks[0m[0;34m,[0m [0mlog_stdout[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 22[0m [0;32mexcept[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 23[0m [0mdiagnostics[0m[0;34m.[0m[0mend_cmd[0m[0;34m([0m[0mcmd_id[0m[0;34m,[0m [0mFalse[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36m_do_run[0;34m(cmd, checks, log_stdout)[0m | |
| [1;32m 93[0m [0ms[0m[0;34m.[0m[0mcommunicate[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 94[0m [0ms[0m[0;34m.[0m[0mstdout[0m[0;34m.[0m[0mclose[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 95[0;31m [0;32mraise[0m [0msubprocess[0m[0;34m.[0m[0mCalledProcessError[0m[0;34m([0m[0mexitcode[0m[0;34m,[0m [0merror_msg[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 96[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 97[0m [0;32mbreak[0m[0;34m[0m[0m | |
| [0;31mCalledProcessError[0m: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-1\tPL:illumina\tPU:NA12878-1\tSM:NA12878-1' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 60000001 80000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 60000001 80000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/12f5566d-0ffc-4e8c-8585-082cf53fca86/tmpmAAwY2/NA12878-1-sort-60000001_80000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/011de5d7-b154-41df-bb14-2949bf5eba97/tmpeVj0HD/NA12878-1-sort-60000001_80000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/12f5566d-0ffc-4e8c-8585-082cf53fca86/tmpmAAwY2/NA12878-1-sort-60000001_80000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/7d11710d-a234-4731-93e4-41908fb6aa72/tmpe22_UI/NA12878-1-sort-60000001_80000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/12f5566d-0ffc-4e8c-8585-082cf53fca86/tmpmAAwY2/NA12878-1-sort-60000001_80000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/12f5566d-0ffc-4e8c-8585-082cf53fca86/tmpmAAwY2/NA12878-1-sort-60000001_80000000.bam /dev/stdin | |
| [W::sam_hdr_parse] duplicated sequence 'GL000216.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000215.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000205.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000219.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000224.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000223.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000195.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000212.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000222.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000200.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000193.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000194.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000225.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000192.1' | |
| duplicating @RG line NA12878-1 | |
| duplicating @PG line bwa | |
| duplicating @SQ line 1 | |
| duplicating @SQ line 2 | |
| duplicating @SQ line 3 | |
| duplicating @SQ line 4 | |
| duplicating @SQ line 5 | |
| duplicating @SQ line 6 | |
| duplicating @SQ line 7 | |
| duplicating @SQ line 8 | |
| duplicating @SQ line 9 | |
| duplicating @SQ line 10 | |
| duplicating @SQ line 11 | |
| duplicating @SQ line 12 | |
| duplicating @SQ line 13 | |
| duplicating @SQ line 14 | |
| duplicating @SQ line 15 | |
| duplicating @SQ line 16 | |
| duplicating @SQ line 17 | |
| duplicating @SQ line 18 | |
| duplicating @SQ line 19 | |
| duplicating @SQ line 20 | |
| duplicating @SQ line 21 | |
| duplicating @SQ line 22 | |
| duplicating @SQ line X | |
| duplicating @SQ line Y | |
| duplicating @SQ line MT | |
| duplicating @SQ line GL000207.1 | |
| duplicating @SQ line GL000226.1 | |
| duplicating @SQ line GL000229.1 | |
| duplicating @SQ line GL000231.1 | |
| duplicating @SQ line GL000210.1 | |
| duplicating @SQ line GL000239.1 | |
| duplicating @SQ line GL000235.1 | |
| duplicating @SQ line GL000201.1 | |
| duplicating @SQ line GL000247.1 | |
| duplicating @SQ line GL000245.1 | |
| duplicating @SQ line GL000197.1 | |
| duplicating @SQ line GL000203.1 | |
| duplicating @SQ line GL000246.1 | |
| duplicating @SQ line GL000249.1 | |
| duplicating @SQ line GL000196.1 | |
| duplicating @SQ line GL000248.1 | |
| duplicating @SQ line GL000244.1 | |
| duplicating @SQ line GL000238.1 | |
| duplicating @SQ line GL000202.1 | |
| duplicating @SQ line GL000234.1 | |
| duplicating @SQ line GL000232.1 | |
| duplicating @SQ line GL000206.1 | |
| duplicating @SQ line GL000240.1 | |
| duplicating @SQ line GL000236.1 | |
| duplicating @SQ line GL000241.1 | |
| duplicating @SQ line GL000243.1 | |
| duplicating @SQ line GL000242.1 | |
| duplicating @SQ line GL000230.1 | |
| duplicating @SQ line GL000237.1 | |
| duplicating @SQ line GL000233.1 | |
| duplicating @SQ line GL000204.1 | |
| duplicating @SQ line GL000198.1 | |
| duplicating @SQ line GL000208.1 | |
| duplicating @SQ line GL000191.1 | |
| duplicating @SQ line GL000227.1 | |
| duplicating @SQ line GL000228.1 | |
| duplicating @SQ line GL000214.1 | |
| duplicating @SQ line GL000221.1 | |
| duplicating @SQ line GL000209.1 | |
| duplicating @SQ line GL000218.1 | |
| duplicating @SQ line GL000220.1 | |
| duplicating @SQ line GL000213.1 | |
| duplicating @SQ line GL000211.1 | |
| duplicating @SQ line GL000199.1 | |
| duplicating @SQ line GL000217.1 | |
| duplicating @SQ line GL000216.1 | |
| duplicating @SQ line GL000215.1 | |
| duplicating @SQ line GL000205.1 | |
| duplicating @SQ line GL000219.1 | |
| duplicating @SQ line GL000224.1 | |
| duplicating @SQ line GL000223.1 | |
| duplicating @SQ line GL000195.1 | |
| duplicating @SQ line GL000212.1 | |
| duplicating @SQ line GL000222.1 | |
| duplicating @SQ line GL000200.1 | |
| duplicating @SQ line GL000193.1 | |
| duplicating @SQ line GL000194.1 | |
| duplicating @SQ line GL000225.1 | |
| duplicating @SQ line GL000192.1 | |
| ' returned non-zero exit status 1 | |
| cat: write error: Broken pipe | |
| 2016-07-28 00:27:42.892 [IPEngineApp] Exception in apply request: | |
| [0;31m[0m | |
| [0;31mCalledProcessError[0mTraceback (most recent call last) | |
| [0;32m<string>[0m in [0;36m<module>[0;34m()[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc[0m in [0;36m__call__[0;34m(self, *args, **kwargs)[0m | |
| [1;32m 71[0m [0;34m[0m[0m | |
| [1;32m 72[0m [0;32mdef[0m [0m__call__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m---> 73[0;31m [0;32mreturn[0m [0mself[0m[0;34m.[0m[0mf[0m[0;34m([0m[0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 74[0m [0;34m[0m[0m | |
| [1;32m 75[0m [0;32mif[0m [0;32mnot[0m [0mpy3compat[0m[0;34m.[0m[0mPY3[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc[0m in [0;36mprocess_alignment[0;34m(*args)[0m | |
| [1;32m 179[0m [0margs[0m [0;34m=[0m [0mipython[0m[0;34m.[0m[0munzip_args[0m[0;34m([0m[0margs[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 180[0m [0;32mwith[0m [0m_setup_logging[0m[0;34m([0m[0margs[0m[0;34m)[0m [0;32mas[0m [0mconfig[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m--> 181[0;31m [0;32mreturn[0m [0mipython[0m[0;34m.[0m[0mzip_args[0m[0;34m([0m[0mapply[0m[0;34m([0m[0msample[0m[0;34m.[0m[0mprocess_alignment[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 182[0m [0;34m[0m[0m | |
| [1;32m 183[0m [0;34m@[0m[0mrequire[0m[0;34m([0m[0malignprep[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc[0m in [0;36mprocess_alignment[0;34m(data, alt_input)[0m | |
| [1;32m 110[0m [0;32mif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0maligner[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 111[0m [0mlogger[0m[0;34m.[0m[0minfo[0m[0;34m([0m[0;34m"Aligning lane %s with %s aligner"[0m [0;34m%[0m [0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"rgnames"[0m[0;34m][0m[0;34m[[0m[0;34m"lane"[0m[0;34m][0m[0;34m,[0m [0maligner[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m--> 112[0;31m [0mdata[0m [0;34m=[0m [0malign_to_sort_bam[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0maligner[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 113[0m [0mdata[0m [0;34m=[0m [0m_add_supplemental_bams[0m[0;34m([0m[0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 114[0m [0;32melif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0mfastq1[0m[0;34m.[0m[0mendswith[0m[0;34m([0m[0;34m".bam"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36malign_to_sort_bam[0;34m(fastq1, fastq2, aligner, data)[0m | |
| [1;32m 62[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 63[0m data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file, | |
| [0;32m---> 64[0;31m names, align_dir, data) | |
| [0m[1;32m 65[0m [0;32mif[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;32mand[0m [0mutils[0m[0;34m.[0m[0mfile_exists[0m[0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 66[0m [0;32mif[0m [0;32mnot[0m [0mdata[0m[0;34m.[0m[0mget[0m[0;34m([0m[0;34m"align_split"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36m_align_from_fastq[0;34m(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)[0m | |
| [1;32m 115[0m [0mconfig[0m [0;34m=[0m [0mdata[0m[0;34m[[0m[0;34m"config"[0m[0;34m][0m[0;34m[0m[0m | |
| [1;32m 116[0m [0malign_fn[0m [0;34m=[0m [0mTOOLS[0m[0;34m[[0m[0maligner[0m[0;34m][0m[0;34m.[0m[0malign_fn[0m[0;34m[0m[0m | |
| [0;32m--> 117[0;31m [0mout[0m [0;34m=[0m [0malign_fn[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0malign_ref[0m[0;34m,[0m [0mnames[0m[0;34m,[0m [0malign_dir[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 118[0m [0;31m# handle align functions that update the main data dictionary in place[0m[0;34m[0m[0;34m[0m[0m | |
| [1;32m 119[0m [0;32mif[0m [0misinstance[0m[0;34m([0m[0mout[0m[0;34m,[0m [0mdict[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36malign_pipe[0;34m(fastq_file, pair_file, ref_file, names, align_dir, data)[0m | |
| [1;32m 145[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 146[0m out_file = _align_mem(fastq_file, pair_file, ref_file, out_file, | |
| [0;32m--> 147[0;31m names, rg_info, data) | |
| [0m[1;32m 148[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;34m=[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 149[0m [0;32mreturn[0m [0mdata[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36m_align_mem[0;34m(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)[0m | |
| [1;32m 155[0m [0mcmd[0m [0;34m=[0m [0;34m"%s | %s"[0m [0;34m%[0m [0;34m([0m[0m_get_bwa_mem_cmd[0m[0;34m([0m[0mdata[0m[0;34m,[0m [0mout_file[0m[0;34m,[0m [0mref_file[0m[0;34m,[0m [0mfastq_file[0m[0;34m,[0m [0mpair_file[0m[0;34m)[0m[0;34m,[0m [0mtobam_cl[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 156[0m do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None, | |
| [0;32m--> 157[0;31m [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)]) | |
| [0m[1;32m 158[0m [0;32mreturn[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 159[0m [0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36mrun[0;34m(cmd, descr, data, checks, region, log_error, log_stdout)[0m | |
| [1;32m 19[0m [0;32mtry[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 20[0m [0mlogger_cl[0m[0;34m.[0m[0mdebug[0m[0;34m([0m[0;34m" "[0m[0;34m.[0m[0mjoin[0m[0;34m([0m[0mstr[0m[0;34m([0m[0mx[0m[0;34m)[0m [0;32mfor[0m [0mx[0m [0;32min[0m [0mcmd[0m[0;34m)[0m [0;32mif[0m [0;32mnot[0m [0misinstance[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mbasestring[0m[0;34m)[0m [0;32melse[0m [0mcmd[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 21[0;31m [0m_do_run[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mchecks[0m[0;34m,[0m [0mlog_stdout[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 22[0m [0;32mexcept[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 23[0m [0mdiagnostics[0m[0;34m.[0m[0mend_cmd[0m[0;34m([0m[0mcmd_id[0m[0;34m,[0m [0mFalse[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36m_do_run[0;34m(cmd, checks, log_stdout)[0m | |
| [1;32m 93[0m [0ms[0m[0;34m.[0m[0mcommunicate[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 94[0m [0ms[0m[0;34m.[0m[0mstdout[0m[0;34m.[0m[0mclose[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 95[0;31m [0;32mraise[0m [0msubprocess[0m[0;34m.[0m[0mCalledProcessError[0m[0;34m([0m[0mexitcode[0m[0;34m,[0m [0merror_msg[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 96[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 97[0m [0;32mbreak[0m[0;34m[0m[0m | |
| [0;31mCalledProcessError[0m: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-1\tPL:illumina\tPU:NA12878-1\tSM:NA12878-1' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 100000001 120000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 100000001 120000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/01ccd89d-561f-4238-8b3b-4f2e34fb548f/tmpfNPArL/NA12878-1-sort-100000001_120000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/a6d6fcb9-d3a4-4778-b984-b0c9fe8b9c7c/tmpiekIbN/NA12878-1-sort-100000001_120000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/01ccd89d-561f-4238-8b3b-4f2e34fb548f/tmpfNPArL/NA12878-1-sort-100000001_120000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/da518b93-a723-4ae6-9c67-6b32e4bbf239/tmpbgWYqv/NA12878-1-sort-100000001_120000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/01ccd89d-561f-4238-8b3b-4f2e34fb548f/tmpfNPArL/NA12878-1-sort-100000001_120000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/01ccd89d-561f-4238-8b3b-4f2e34fb548f/tmpfNPArL/NA12878-1-sort-100000001_120000000.bam /dev/stdin | |
| duplicating @SQ line GL000199.1 | |
| duplicating @SQ line GL000217.1 | |
| duplicating @SQ line GL000216.1 | |
| duplicating @SQ line GL000215.1 | |
| duplicating @SQ line GL000205.1 | |
| duplicating @SQ line GL000219.1 | |
| duplicating @SQ line GL000224.1 | |
| duplicating @SQ line GL000223.1 | |
| duplicating @SQ line GL000195.1 | |
| duplicating @SQ line GL000212.1 | |
| duplicating @SQ line GL000222.1 | |
| duplicating @SQ line GL000200.1 | |
| duplicating @SQ line GL000193.1 | |
| duplicating @SQ line GL000194.1 | |
| duplicating @SQ line GL000225.1 | |
| duplicating @SQ line GL000192.1 | |
| duplicating @SQ line 1 | |
| duplicating @SQ line 2 | |
| duplicating @SQ line 3 | |
| duplicating @SQ line 4 | |
| duplicating @SQ line 5 | |
| duplicating @SQ line 6 | |
| duplicating @SQ line 7 | |
| duplicating @SQ line 8 | |
| duplicating @SQ line 9 | |
| duplicating @SQ line 10 | |
| duplicating @SQ line 11 | |
| duplicating @SQ line 12 | |
| duplicating @SQ line 13 | |
| duplicating @SQ line 14 | |
| duplicating @SQ line 15 | |
| duplicating @SQ line 16 | |
| duplicating @SQ line 17 | |
| duplicating @SQ line 18 | |
| duplicating @SQ line 19 | |
| duplicating @SQ line 20 | |
| duplicating @SQ line 21 | |
| duplicating @SQ line 22 | |
| duplicating @SQ line X | |
| duplicating @SQ line Y | |
| duplicating @SQ line MT | |
| duplicating @SQ line GL000207.1 | |
| duplicating @SQ line GL000226.1 | |
| duplicating @SQ line GL000229.1 | |
| duplicating @SQ line GL000231.1 | |
| duplicating @SQ line GL000210.1 | |
| duplicating @SQ line GL000239.1 | |
| duplicating @SQ line GL000235.1 | |
| duplicating @SQ line GL000201.1 | |
| duplicating @SQ line GL000247.1 | |
| duplicating @SQ line GL000245.1 | |
| duplicating @SQ line GL000197.1 | |
| duplicating @SQ line GL000203.1 | |
| duplicating @SQ line GL000246.1 | |
| duplicating @SQ line GL000249.1 | |
| duplicating @SQ line GL000196.1 | |
| duplicating @SQ line GL000248.1 | |
| duplicating @SQ line GL000244.1 | |
| duplicating @SQ line GL000238.1 | |
| duplicating @SQ line GL000202.1 | |
| duplicating @SQ line GL000234.1 | |
| duplicating @SQ line GL000232.1 | |
| duplicating @SQ line GL000206.1 | |
| duplicating @SQ line GL000240.1 | |
| duplicating @SQ line GL000236.1 | |
| duplicating @SQ line GL000241.1 | |
| duplicating @SQ line GL000243.1 | |
| duplicating @SQ line GL000242.1 | |
| duplicating @SQ line GL000230.1 | |
| duplicating @SQ line GL000237.1 | |
| duplicating @SQ line GL000233.1 | |
| duplicating @SQ line GL000204.1 | |
| duplicating @SQ line GL000198.1 | |
| duplicating @SQ line GL000208.1 | |
| duplicating @SQ line GL000191.1 | |
| duplicating @SQ line GL000227.1 | |
| duplicating @SQ line GL000228.1 | |
| duplicating @SQ line GL000214.1 | |
| duplicating @SQ line GL000221.1 | |
| duplicating @SQ line GL000209.1 | |
| duplicating @SQ line GL000218.1 | |
| duplicating @SQ line GL000220.1 | |
| duplicating @SQ line GL000213.1 | |
| duplicating @SQ line GL000211.1 | |
| duplicating @SQ line GL000199.1 | |
| duplicating @SQ line GL000217.1 | |
| duplicating @SQ line GL000216.1 | |
| duplicating @SQ line GL000215.1 | |
| duplicating @SQ line GL000205.1 | |
| duplicating @SQ line GL000219.1 | |
| duplicating @SQ line GL000224.1 | |
| duplicating @SQ line GL000223.1 | |
| duplicating @SQ line GL000195.1 | |
| duplicating @SQ line GL000212.1 | |
| duplicating @SQ line GL000222.1 | |
| duplicating @SQ line GL000200.1 | |
| duplicating @SQ line GL000193.1 | |
| duplicating @SQ line GL000194.1 | |
| duplicating @SQ line GL000225.1 | |
| duplicating @SQ line GL000192.1 | |
| ' returned non-zero exit status 1 | |
| cat: write error: Broken pipe | |
| 2016-07-28 00:28:05.672 [IPEngineApp] Exception in apply request: | |
| [0;31m[0m | |
| [0;31mCalledProcessError[0mTraceback (most recent call last) | |
| [0;32m<string>[0m in [0;36m<module>[0;34m()[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc[0m in [0;36m__call__[0;34m(self, *args, **kwargs)[0m | |
| [1;32m 71[0m [0;34m[0m[0m | |
| [1;32m 72[0m [0;32mdef[0m [0m__call__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m---> 73[0;31m [0;32mreturn[0m [0mself[0m[0;34m.[0m[0mf[0m[0;34m([0m[0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 74[0m [0;34m[0m[0m | |
| [1;32m 75[0m [0;32mif[0m [0;32mnot[0m [0mpy3compat[0m[0;34m.[0m[0mPY3[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc[0m in [0;36mprocess_alignment[0;34m(*args)[0m | |
| [1;32m 179[0m [0margs[0m [0;34m=[0m [0mipython[0m[0;34m.[0m[0munzip_args[0m[0;34m([0m[0margs[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 180[0m [0;32mwith[0m [0m_setup_logging[0m[0;34m([0m[0margs[0m[0;34m)[0m [0;32mas[0m [0mconfig[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m--> 181[0;31m [0;32mreturn[0m [0mipython[0m[0;34m.[0m[0mzip_args[0m[0;34m([0m[0mapply[0m[0;34m([0m[0msample[0m[0;34m.[0m[0mprocess_alignment[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 182[0m [0;34m[0m[0m | |
| [1;32m 183[0m [0;34m@[0m[0mrequire[0m[0;34m([0m[0malignprep[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc[0m in [0;36mprocess_alignment[0;34m(data, alt_input)[0m | |
| [1;32m 110[0m [0;32mif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0maligner[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 111[0m [0mlogger[0m[0;34m.[0m[0minfo[0m[0;34m([0m[0;34m"Aligning lane %s with %s aligner"[0m [0;34m%[0m [0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"rgnames"[0m[0;34m][0m[0;34m[[0m[0;34m"lane"[0m[0;34m][0m[0;34m,[0m [0maligner[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m--> 112[0;31m [0mdata[0m [0;34m=[0m [0malign_to_sort_bam[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0maligner[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 113[0m [0mdata[0m [0;34m=[0m [0m_add_supplemental_bams[0m[0;34m([0m[0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 114[0m [0;32melif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0mfastq1[0m[0;34m.[0m[0mendswith[0m[0;34m([0m[0;34m".bam"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36malign_to_sort_bam[0;34m(fastq1, fastq2, aligner, data)[0m | |
| [1;32m 62[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 63[0m data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file, | |
| [0;32m---> 64[0;31m names, align_dir, data) | |
| [0m[1;32m 65[0m [0;32mif[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;32mand[0m [0mutils[0m[0;34m.[0m[0mfile_exists[0m[0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 66[0m [0;32mif[0m [0;32mnot[0m [0mdata[0m[0;34m.[0m[0mget[0m[0;34m([0m[0;34m"align_split"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36m_align_from_fastq[0;34m(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)[0m | |
| [1;32m 115[0m [0mconfig[0m [0;34m=[0m [0mdata[0m[0;34m[[0m[0;34m"config"[0m[0;34m][0m[0;34m[0m[0m | |
| [1;32m 116[0m [0malign_fn[0m [0;34m=[0m [0mTOOLS[0m[0;34m[[0m[0maligner[0m[0;34m][0m[0;34m.[0m[0malign_fn[0m[0;34m[0m[0m | |
| [0;32m--> 117[0;31m [0mout[0m [0;34m=[0m [0malign_fn[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0malign_ref[0m[0;34m,[0m [0mnames[0m[0;34m,[0m [0malign_dir[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 118[0m [0;31m# handle align functions that update the main data dictionary in place[0m[0;34m[0m[0;34m[0m[0m | |
| [1;32m 119[0m [0;32mif[0m [0misinstance[0m[0;34m([0m[0mout[0m[0;34m,[0m [0mdict[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36malign_pipe[0;34m(fastq_file, pair_file, ref_file, names, align_dir, data)[0m | |
| [1;32m 145[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 146[0m out_file = _align_mem(fastq_file, pair_file, ref_file, out_file, | |
| [0;32m--> 147[0;31m names, rg_info, data) | |
| [0m[1;32m 148[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;34m=[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 149[0m [0;32mreturn[0m [0mdata[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36m_align_mem[0;34m(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)[0m | |
| [1;32m 155[0m [0mcmd[0m [0;34m=[0m [0;34m"%s | %s"[0m [0;34m%[0m [0;34m([0m[0m_get_bwa_mem_cmd[0m[0;34m([0m[0mdata[0m[0;34m,[0m [0mout_file[0m[0;34m,[0m [0mref_file[0m[0;34m,[0m [0mfastq_file[0m[0;34m,[0m [0mpair_file[0m[0;34m)[0m[0;34m,[0m [0mtobam_cl[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 156[0m do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None, | |
| [0;32m--> 157[0;31m [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)]) | |
| [0m[1;32m 158[0m [0;32mreturn[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 159[0m [0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36mrun[0;34m(cmd, descr, data, checks, region, log_error, log_stdout)[0m | |
| [1;32m 19[0m [0;32mtry[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 20[0m [0mlogger_cl[0m[0;34m.[0m[0mdebug[0m[0;34m([0m[0;34m" "[0m[0;34m.[0m[0mjoin[0m[0;34m([0m[0mstr[0m[0;34m([0m[0mx[0m[0;34m)[0m [0;32mfor[0m [0mx[0m [0;32min[0m [0mcmd[0m[0;34m)[0m [0;32mif[0m [0;32mnot[0m [0misinstance[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mbasestring[0m[0;34m)[0m [0;32melse[0m [0mcmd[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 21[0;31m [0m_do_run[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mchecks[0m[0;34m,[0m [0mlog_stdout[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 22[0m [0;32mexcept[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 23[0m [0mdiagnostics[0m[0;34m.[0m[0mend_cmd[0m[0;34m([0m[0mcmd_id[0m[0;34m,[0m [0mFalse[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36m_do_run[0;34m(cmd, checks, log_stdout)[0m | |
| [1;32m 93[0m [0ms[0m[0;34m.[0m[0mcommunicate[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 94[0m [0ms[0m[0;34m.[0m[0mstdout[0m[0;34m.[0m[0mclose[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 95[0;31m [0;32mraise[0m [0msubprocess[0m[0;34m.[0m[0mCalledProcessError[0m[0;34m([0m[0mexitcode[0m[0;34m,[0m [0merror_msg[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 96[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 97[0m [0;32mbreak[0m[0;34m[0m[0m | |
| [0;31mCalledProcessError[0m: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-1\tPL:illumina\tPU:NA12878-1\tSM:NA12878-1' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 80000001 100000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 80000001 100000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/f36686cb-b5c9-4b34-92c0-6645e89529f8/tmpiF_JQm/NA12878-1-sort-80000001_100000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/0445b705-698a-4810-8f4c-166804830938/tmpE9lDEw/NA12878-1-sort-80000001_100000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/f36686cb-b5c9-4b34-92c0-6645e89529f8/tmpiF_JQm/NA12878-1-sort-80000001_100000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/71945eff-862b-4166-a0c7-72bc6f9b50ca/tmp3xwsIG/NA12878-1-sort-80000001_100000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/f36686cb-b5c9-4b34-92c0-6645e89529f8/tmpiF_JQm/NA12878-1-sort-80000001_100000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/f36686cb-b5c9-4b34-92c0-6645e89529f8/tmpiF_JQm/NA12878-1-sort-80000001_100000000.bam /dev/stdin | |
| [W::sam_hdr_parse] duplicated sequence 'GL000216.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000215.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000205.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000219.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000224.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000223.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000195.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000212.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000222.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000200.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000193.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000194.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000225.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000192.1' | |
| duplicating @RG line NA12878-1 | |
| duplicating @PG line bwa | |
| duplicating @SQ line 1 | |
| duplicating @SQ line 2 | |
| duplicating @SQ line 3 | |
| duplicating @SQ line 4 | |
| duplicating @SQ line 5 | |
| duplicating @SQ line 6 | |
| duplicating @SQ line 7 | |
| duplicating @SQ line 8 | |
| duplicating @SQ line 9 | |
| duplicating @SQ line 10 | |
| duplicating @SQ line 11 | |
| duplicating @SQ line 12 | |
| duplicating @SQ line 13 | |
| duplicating @SQ line 14 | |
| duplicating @SQ line 15 | |
| duplicating @SQ line 16 | |
| duplicating @SQ line 17 | |
| duplicating @SQ line 18 | |
| duplicating @SQ line 19 | |
| duplicating @SQ line 20 | |
| duplicating @SQ line 21 | |
| duplicating @SQ line 22 | |
| duplicating @SQ line X | |
| duplicating @SQ line Y | |
| duplicating @SQ line MT | |
| duplicating @SQ line GL000207.1 | |
| duplicating @SQ line GL000226.1 | |
| duplicating @SQ line GL000229.1 | |
| duplicating @SQ line GL000231.1 | |
| duplicating @SQ line GL000210.1 | |
| duplicating @SQ line GL000239.1 | |
| duplicating @SQ line GL000235.1 | |
| duplicating @SQ line GL000201.1 | |
| duplicating @SQ line GL000247.1 | |
| duplicating @SQ line GL000245.1 | |
| duplicating @SQ line GL000197.1 | |
| duplicating @SQ line GL000203.1 | |
| duplicating @SQ line GL000246.1 | |
| duplicating @SQ line GL000249.1 | |
| duplicating @SQ line GL000196.1 | |
| duplicating @SQ line GL000248.1 | |
| duplicating @SQ line GL000244.1 | |
| duplicating @SQ line GL000238.1 | |
| duplicating @SQ line GL000202.1 | |
| duplicating @SQ line GL000234.1 | |
| duplicating @SQ line GL000232.1 | |
| duplicating @SQ line GL000206.1 | |
| duplicating @SQ line GL000240.1 | |
| duplicating @SQ line GL000236.1 | |
| duplicating @SQ line GL000241.1 | |
| duplicating @SQ line GL000243.1 | |
| duplicating @SQ line GL000242.1 | |
| duplicating @SQ line GL000230.1 | |
| duplicating @SQ line GL000237.1 | |
| duplicating @SQ line GL000233.1 | |
| duplicating @SQ line GL000204.1 | |
| duplicating @SQ line GL000198.1 | |
| duplicating @SQ line GL000208.1 | |
| duplicating @SQ line GL000191.1 | |
| duplicating @SQ line GL000227.1 | |
| duplicating @SQ line GL000228.1 | |
| duplicating @SQ line GL000214.1 | |
| duplicating @SQ line GL000221.1 | |
| duplicating @SQ line GL000209.1 | |
| duplicating @SQ line GL000218.1 | |
| duplicating @SQ line GL000220.1 | |
| duplicating @SQ line GL000213.1 | |
| duplicating @SQ line GL000211.1 | |
| duplicating @SQ line GL000199.1 | |
| duplicating @SQ line GL000217.1 | |
| duplicating @SQ line GL000216.1 | |
| duplicating @SQ line GL000215.1 | |
| duplicating @SQ line GL000205.1 | |
| duplicating @SQ line GL000219.1 | |
| duplicating @SQ line GL000224.1 | |
| duplicating @SQ line GL000223.1 | |
| duplicating @SQ line GL000195.1 | |
| duplicating @SQ line GL000212.1 | |
| duplicating @SQ line GL000222.1 | |
| duplicating @SQ line GL000200.1 | |
| duplicating @SQ line GL000193.1 | |
| duplicating @SQ line GL000194.1 | |
| duplicating @SQ line GL000225.1 | |
| duplicating @SQ line GL000192.1 | |
| ' returned non-zero exit status 1 | |
| cat: write error: Broken pipe | |
| 2016-07-28 00:28:53.469 [IPEngineApp] Exception in apply request: | |
| [0;31m[0m | |
| [0;31mCalledProcessError[0mTraceback (most recent call last) | |
| [0;32m<string>[0m in [0;36m<module>[0;34m()[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc[0m in [0;36m__call__[0;34m(self, *args, **kwargs)[0m | |
| [1;32m 71[0m [0;34m[0m[0m | |
| [1;32m 72[0m [0;32mdef[0m [0m__call__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m---> 73[0;31m [0;32mreturn[0m [0mself[0m[0;34m.[0m[0mf[0m[0;34m([0m[0;34m*[0m[0margs[0m[0;34m,[0m [0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 74[0m [0;34m[0m[0m | |
| [1;32m 75[0m [0;32mif[0m [0;32mnot[0m [0mpy3compat[0m[0;34m.[0m[0mPY3[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc[0m in [0;36mprocess_alignment[0;34m(*args)[0m | |
| [1;32m 179[0m [0margs[0m [0;34m=[0m [0mipython[0m[0;34m.[0m[0munzip_args[0m[0;34m([0m[0margs[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 180[0m [0;32mwith[0m [0m_setup_logging[0m[0;34m([0m[0margs[0m[0;34m)[0m [0;32mas[0m [0mconfig[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m--> 181[0;31m [0;32mreturn[0m [0mipython[0m[0;34m.[0m[0mzip_args[0m[0;34m([0m[0mapply[0m[0;34m([0m[0msample[0m[0;34m.[0m[0mprocess_alignment[0m[0;34m,[0m [0;34m*[0m[0margs[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 182[0m [0;34m[0m[0m | |
| [1;32m 183[0m [0;34m@[0m[0mrequire[0m[0;34m([0m[0malignprep[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc[0m in [0;36mprocess_alignment[0;34m(data, alt_input)[0m | |
| [1;32m 110[0m [0;32mif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0maligner[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 111[0m [0mlogger[0m[0;34m.[0m[0minfo[0m[0;34m([0m[0;34m"Aligning lane %s with %s aligner"[0m [0;34m%[0m [0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"rgnames"[0m[0;34m][0m[0;34m[[0m[0;34m"lane"[0m[0;34m][0m[0;34m,[0m [0maligner[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m--> 112[0;31m [0mdata[0m [0;34m=[0m [0malign_to_sort_bam[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0maligner[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 113[0m [0mdata[0m [0;34m=[0m [0m_add_supplemental_bams[0m[0;34m([0m[0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 114[0m [0;32melif[0m [0mfastq1[0m [0;32mand[0m [0mobjectstore[0m[0;34m.[0m[0mfile_exists_or_remote[0m[0;34m([0m[0mfastq1[0m[0;34m)[0m [0;32mand[0m [0mfastq1[0m[0;34m.[0m[0mendswith[0m[0;34m([0m[0;34m".bam"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36malign_to_sort_bam[0;34m(fastq1, fastq2, aligner, data)[0m | |
| [1;32m 62[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 63[0m data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file, | |
| [0;32m---> 64[0;31m names, align_dir, data) | |
| [0m[1;32m 65[0m [0;32mif[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;32mand[0m [0mutils[0m[0;34m.[0m[0mfile_exists[0m[0;34m([0m[0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 66[0m [0;32mif[0m [0;32mnot[0m [0mdata[0m[0;34m.[0m[0mget[0m[0;34m([0m[0;34m"align_split"[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc[0m in [0;36m_align_from_fastq[0;34m(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)[0m | |
| [1;32m 115[0m [0mconfig[0m [0;34m=[0m [0mdata[0m[0;34m[[0m[0;34m"config"[0m[0;34m][0m[0;34m[0m[0m | |
| [1;32m 116[0m [0malign_fn[0m [0;34m=[0m [0mTOOLS[0m[0;34m[[0m[0maligner[0m[0;34m][0m[0;34m.[0m[0malign_fn[0m[0;34m[0m[0m | |
| [0;32m--> 117[0;31m [0mout[0m [0;34m=[0m [0malign_fn[0m[0;34m([0m[0mfastq1[0m[0;34m,[0m [0mfastq2[0m[0;34m,[0m [0malign_ref[0m[0;34m,[0m [0mnames[0m[0;34m,[0m [0malign_dir[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 118[0m [0;31m# handle align functions that update the main data dictionary in place[0m[0;34m[0m[0;34m[0m[0m | |
| [1;32m 119[0m [0;32mif[0m [0misinstance[0m[0;34m([0m[0mout[0m[0;34m,[0m [0mdict[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36malign_pipe[0;34m(fastq_file, pair_file, ref_file, names, align_dir, data)[0m | |
| [1;32m 145[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 146[0m out_file = _align_mem(fastq_file, pair_file, ref_file, out_file, | |
| [0;32m--> 147[0;31m names, rg_info, data) | |
| [0m[1;32m 148[0m [0mdata[0m[0;34m[[0m[0;34m"work_bam"[0m[0;34m][0m [0;34m=[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 149[0m [0;32mreturn[0m [0mdata[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc[0m in [0;36m_align_mem[0;34m(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)[0m | |
| [1;32m 155[0m [0mcmd[0m [0;34m=[0m [0;34m"%s | %s"[0m [0;34m%[0m [0;34m([0m[0m_get_bwa_mem_cmd[0m[0;34m([0m[0mdata[0m[0;34m,[0m [0mout_file[0m[0;34m,[0m [0mref_file[0m[0;34m,[0m [0mfastq_file[0m[0;34m,[0m [0mpair_file[0m[0;34m)[0m[0;34m,[0m [0mtobam_cl[0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 156[0m do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None, | |
| [0;32m--> 157[0;31m [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)]) | |
| [0m[1;32m 158[0m [0;32mreturn[0m [0mout_file[0m[0;34m[0m[0m | |
| [1;32m 159[0m [0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36mrun[0;34m(cmd, descr, data, checks, region, log_error, log_stdout)[0m | |
| [1;32m 19[0m [0;32mtry[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 20[0m [0mlogger_cl[0m[0;34m.[0m[0mdebug[0m[0;34m([0m[0;34m" "[0m[0;34m.[0m[0mjoin[0m[0;34m([0m[0mstr[0m[0;34m([0m[0mx[0m[0;34m)[0m [0;32mfor[0m [0mx[0m [0;32min[0m [0mcmd[0m[0;34m)[0m [0;32mif[0m [0;32mnot[0m [0misinstance[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mbasestring[0m[0;34m)[0m [0;32melse[0m [0mcmd[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 21[0;31m [0m_do_run[0m[0;34m([0m[0mcmd[0m[0;34m,[0m [0mchecks[0m[0;34m,[0m [0mlog_stdout[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 22[0m [0;32mexcept[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 23[0m [0mdiagnostics[0m[0;34m.[0m[0mend_cmd[0m[0;34m([0m[0mcmd_id[0m[0;34m,[0m [0mFalse[0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m/home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc[0m in [0;36m_do_run[0;34m(cmd, checks, log_stdout)[0m | |
| [1;32m 93[0m [0ms[0m[0;34m.[0m[0mcommunicate[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [1;32m 94[0m [0ms[0m[0;34m.[0m[0mstdout[0m[0;34m.[0m[0mclose[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m | |
| [0;32m---> 95[0;31m [0;32mraise[0m [0msubprocess[0m[0;34m.[0m[0mCalledProcessError[0m[0;34m([0m[0mexitcode[0m[0;34m,[0m [0merror_msg[0m[0;34m)[0m[0;34m[0m[0m | |
| [0m[1;32m 96[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0m | |
| [1;32m 97[0m [0;32mbreak[0m[0;34m[0m[0m | |
| [0;31mCalledProcessError[0m: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-2\tPL:illumina\tPU:NA12878-2\tSM:NA12878-2' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 160000001 176313700) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 160000001 176313700) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/08751093-9024-4609-9794-a31ef68c3151/tmpCzS63B/NA12878-2-sort-160000001_176313700-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/01490ba2-57c3-42b9-a1cd-50145333b5f2/tmp1C0LJg/NA12878-2-sort-160000001_176313700-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/08751093-9024-4609-9794-a31ef68c3151/tmpCzS63B/NA12878-2-sort-160000001_176313700-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/ad8af680-18c4-49e8-84fe-0750516cce50/tmpYmIxfA/NA12878-2-sort-160000001_176313700-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/08751093-9024-4609-9794-a31ef68c3151/tmpCzS63B/NA12878-2-sort-160000001_176313700-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/08751093-9024-4609-9794-a31ef68c3151/tmpCzS63B/NA12878-2-sort-160000001_176313700.bam /dev/stdin | |
| [W::sam_hdr_parse] duplicated sequence 'GL000216.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000215.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000205.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000219.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000224.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000223.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000195.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000212.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000222.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000200.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000193.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000194.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000225.1' | |
| [W::sam_hdr_parse] duplicated sequence 'GL000192.1' | |
| duplicating @RG line NA12878-2 | |
| duplicating @PG line bwa | |
| duplicating @SQ line 1 | |
| duplicating @SQ line 2 | |
| duplicating @SQ line 3 | |
| duplicating @SQ line 4 | |
| duplicating @SQ line 5 | |
| duplicating @SQ line 6 | |
| duplicating @SQ line 7 | |
| duplicating @SQ line 8 | |
| duplicating @SQ line 9 | |
| duplicating @SQ line 10 | |
| duplicating @SQ line 11 | |
| duplicating @SQ line 12 | |
| duplicating @SQ line 13 | |
| duplicating @SQ line 14 | |
| duplicating @SQ line 15 | |
| duplicating @SQ line 16 | |
| duplicating @SQ line 17 | |
| duplicating @SQ line 18 | |
| duplicating @SQ line 19 | |
| duplicating @SQ line 20 | |
| duplicating @SQ line 21 | |
| duplicating @SQ line 22 | |
| duplicating @SQ line X | |
| duplicating @SQ line Y | |
| duplicating @SQ line MT | |
| duplicating @SQ line GL000207.1 | |
| duplicating @SQ line GL000226.1 | |
| duplicating @SQ line GL000229.1 | |
| duplicating @SQ line GL000231.1 | |
| duplicating @SQ line GL000210.1 | |
| duplicating @SQ line GL000239.1 | |
| duplicating @SQ line GL000235.1 | |
| duplicating @SQ line GL000201.1 | |
| duplicating @SQ line GL000247.1 | |
| duplicating @SQ line GL000245.1 | |
| duplicating @SQ line GL000197.1 | |
| duplicating @SQ line GL000203.1 | |
| duplicating @SQ line GL000246.1 | |
| duplicating @SQ line GL000249.1 | |
| duplicating @SQ line GL000196.1 | |
| duplicating @SQ line GL000248.1 | |
| duplicating @SQ line GL000244.1 | |
| duplicating @SQ line GL000238.1 | |
| duplicating @SQ line GL000202.1 | |
| duplicating @SQ line GL000234.1 | |
| duplicating @SQ line GL000232.1 | |
| duplicating @SQ line GL000206.1 | |
| duplicating @SQ line GL000240.1 | |
| duplicating @SQ line GL000236.1 | |
| duplicating @SQ line GL000241.1 | |
| duplicating @SQ line GL000243.1 | |
| duplicating @SQ line GL000242.1 | |
| duplicating @SQ line GL000230.1 | |
| duplicating @SQ line GL000237.1 | |
| duplicating @SQ line GL000233.1 | |
| duplicating @SQ line GL000204.1 | |
| duplicating @SQ line GL000198.1 | |
| duplicating @SQ line GL000208.1 | |
| duplicating @SQ line GL000191.1 | |
| duplicating @SQ line GL000227.1 | |
| duplicating @SQ line GL000228.1 | |
| duplicating @SQ line GL000214.1 | |
| duplicating @SQ line GL000221.1 | |
| duplicating @SQ line GL000209.1 | |
| duplicating @SQ line GL000218.1 | |
| duplicating @SQ line GL000220.1 | |
| duplicating @SQ line GL000213.1 | |
| duplicating @SQ line GL000211.1 | |
| duplicating @SQ line GL000199.1 | |
| duplicating @SQ line GL000217.1 | |
| duplicating @SQ line GL000216.1 | |
| duplicating @SQ line GL000215.1 | |
| duplicating @SQ line GL000205.1 | |
| duplicating @SQ line GL000219.1 | |
| duplicating @SQ line GL000224.1 | |
| duplicating @SQ line GL000223.1 | |
| duplicating @SQ line GL000195.1 | |
| duplicating @SQ line GL000212.1 | |
| duplicating @SQ line GL000222.1 | |
| duplicating @SQ line GL000200.1 | |
| duplicating @SQ line GL000193.1 | |
| duplicating @SQ line GL000194.1 | |
| duplicating @SQ line GL000225.1 | |
| duplicating @SQ line GL000192.1 | |
| ' returned non-zero exit status 1 | |
| slurmstepd: *** JOB 30513 ON spartan063 CANCELLED AT 2016-07-28T00:29:07 *** |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment