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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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variant calling error #1114

Closed pengxiao78 closed 8 years ago

pengxiao78 commented 8 years ago

Hi Brad, When I was using both svcaller: cnvkit and ensemble (>=2) for variantcaller:

2015-11-16T16:50Z] _.edu: Timing: structural variation initial [2015-11-16T16:50Z] .edu: multiprocessing: detect_sv [2015-11-16T16:50Z] .edu: multiprocessing: finalize_sv [2015-11-16T18:49Z] .edu: Timing: alignment post-processing [2015-11-16T18:49Z] .edu: ipython: piped_bamprep [2015-11-18T02:50Z] .edu: Timing: variant calling [2015-11-18T02:51Z] .edu: ipython: variantcall_sample [2015-11-18T03:14Z] .edu: Uncaught exception occurred Traceback (most recent call last): File "./bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run _do_run(cmd, checks, log_stdout) File "./bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run raise subprocess.CalledProcessError(exitcode, error_msg) CalledProcessError: Command 'set -o pipefail; export VAR_DICT_OPTS='-Xms750m -Xmx3000m -XX:+UseSerialGC -Djava.io.tmpdir=/project/work/vardict/1/tx/tmpEMlNPx' && vardict-java -G ./bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -f 0.1 -N 1483FFPE -b "/project/work/bamprep/1483FFPE/1/21_2015-11-05_project-merged-sort-1_62039291_93059007-prep.bam|/project/work/bamprep/1483Germ/1/22_2015-11-05_project-merged-sort-1_62039291_93059007-prep.bam" -c 1 -S 2 -E 3 -g 4 /project/work/vardict/1/batch05-1_62039291_93059007-raw-regions-regionlimit.bed | testsomatic.R | var2vcf_paired.pl -M -P 0.9 -m 4.25 -f 0.1 -N "1483FFPE|1483Germ" | bcftools filter -m '+' -s 'REJECT' -e 'STATUS !~ "._Somatic"' 2> /dev/null | ./bcbio/anaconda/bin/py -x 'bcbio.variation.vardict.depth_freq_filter(x, 0, "bwa")' | sed 's/.Somatic\/Somatic/' | sed 's/REJECT,Description=".">/REJECT,Description="Not Somatic via VarDict">/' | ./bcbio/anaconda/bin/py -x 'bcbio.variation.freebayes.call_somatic(x)' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDX]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | ./bcbio/bin/vcfstreamsort | bgzip -c > /project/work/vardict/1/tx/tmpEMlNPx/batch05-1_62039291_93059007-raw.vcf.gz 2b405b5ef000-2b405b5f0000 ---p 00000000 00:00 0 2b405b5f0000-2b405b7f0000 rw-p 00000000 00:00 0 2b405b7f0000-2b405b7f1000 ---p 00000000 00:00 0 2b405b7f1000-2b405b9f1000 rw-p 00000000 00:00 0 2b405b9f1000-2b405b9f2000 ---p 00000000 00:00 0 2b405b9f2000-2b405bbf2000 rw-p 00000000 00:00 0 2b405bbf2000-2b405bbf3000 ---p 00000000 00:00 0 2b405bbf3000-2b405bdf3000 rw-p 00000000 00:00 0 2b405bdf3000-2b405bdf4000 ---p 00000000 00:00 0 2b405bdf4000-2b405bff4000 rw-p 00000000 00:00 0 2b405bff4000-2b405bff5000 ---p 00000000 00:00 0 2b405bff5000-2b405c1f5000 rw-p 00000000 00:00 0 2b405c1f5000-2b405c1f6000 ---p 00000000 00:00 0 2b405c1f6000-2b405c3f6000 rw-p 00000000 00:00 0 2b405c3f6000-2b405c3f7000 ---p 00000000 00:00 0 2b405c3f7000-2b405c5f7000 rw-p 00000000 00:00 0 2b405c5f7000-2b405c5f8000 ---p 00000000 00:00 0 2b405c5f8000-2b405c7f8000 rw-p 00000000 00:00 0 2b405c7f8000-2b405c7f9000 ---p 00000000 00:00 0 2b405c7f9000-2b405c9f9000 rw-p 00000000 00:00 0 2b405c9f9000-2b405c9fa000 ---p 00000000 00:00 0 2b405c9fa000-2b405cbfa000 rw-p 00000000 00:00 0 2b405cbfa000-2b405cbfb000 ---p 00000000 00:00 0 2b405cbfb000-2b405cdfb000 rw-p 00000000 00:00 0 2b405cdfb000-2b405cdfc000 ---p 00000000 00:00 0 2b405cdfc000-2b405cffc000 rw-p 00000000 00:00 0 2b405cffc000-2b405cffd000 ---p 00000000 00:00 0 2b405cffd000-2b405d1fd000 rw-p 00000000 00:00 0 2b405d1fd000-2b405d1fe000 ---p 00000000 00:00 0 2b405d1fe000-2b405d3fe000 rw-p 00000000 00:00 0 2b405d3fe000-2b405d3ff000 ---p 00000000 00:00 0 2b405d3ff000-2b405d5ff000 rw-p 00000000 00:00 0 2b405d5ff000-2b405d600000 ---p 00000000 00:00 0 2b405d600000-2b405d800000 rw-p 00000000 00:00 0 2b405d800000-2b405d801000 ---p 00000000 00:00 0 2b405d801000-2b405da01000 rw-p 00000000 00:00 0 2b405da01000-2b405da02000 ---p 00000000 00:00 0 2b405da02000-2b405dc02000 rw-p 00000000 00:00 0 2b405dc02000-2b405dc03000 ---p 00000000 00:00 0 2b405dc03000-2b405de03000 rw-p 00000000 00:00 0 2b405de03000-2b405de04000 ---p 00000000 00:00 0 2b405de04000-2b405e004000 rw-p 00000000 00:00 0 2b405e004000-2b405e005000 ---p 00000000 00:00 0 2b405e005000-2b405e205000 rw-p 00000000 00:00 0 2b405e205000-2b405e206000 ---p 00000000 00:00 0 2b405e206000-2b405e406000 rw-p 00000000 00:00 0 2b405e406000-2b405e407000 ---p 00000000 00:00 0 2b405e407000-2b405e607000 rw-p 00000000 00:00 0 2b405e607000-2b405e608000 ---p 00000000 00:00 0 2b405e608000-2b405e808000 rw-p 00000000 00:00 0 2b405e808000-2b405e809000 ---p 00000000 00:00 0 2b405e809000-2b405ea09000 rw-p 00000000 00:00 0 2b405ea09000-2b405ea0a000 ---p 00000000 00:00 0 2b405ea0a000-2b405ec0a000 rw-p 00000000 00:00 0 2b405ec0a000-2b405ec0b000 ---p 00000000 00:00 0 2b405ec0b000-2b405ee0b000 rw-p 00000000 00:00 0 2b405ee0b000-2b405ee0c000 ---p 00000000 00:00 0 2b405ee0c000-2b405f00c000 rw-p 00000000 00:00 0 2b405f00c000-2b405f00d000 ---p 00000000 00:00 0 2b405f00d000-2b405f20d000 rw-p 00000000 00:00 0 2b405f20d000-2b405f20e000 ---p 00000000 00:00 0 2b405f20e000-2b405f40e000 rw-p 00000000 00:00 0 2b405f40e000-2b405f40f000 ---p 00000000 00:00 0 2b405f40f000-2b405f60f000 rw-p 00000000 00:00 0 2b405f60f000-2b405f610000 ---p 00000000 00:00 0 2b405f610000-2b405f810000 rw-p 00000000 00:00 0 2b405f810000-2b405f811000 ---p 00000000 00:00 0 2b405f811000-2b405fa11000 rw-p 00000000 00:00 0 2b405fa11000-2b405fa12000 ---p 00000000 00:00 0 2b405fa12000-2b405fc12000 rw-p 00000000 00:00 0 2b405fc12000-2b405fc13000 ---p 00000000 00:00 0 2b405fc13000-2b405fe13000 rw-p 00000000 00:00 0 2b405fe13000-2b405fe14000 ---p 00000000 00:00 0 2b405fe14000-2b4060014000 rw-p 00000000 00:00 0 2b4060014000-2b4060015000 ---p 00000000 00:00 0 2b4060015000-2b4060215000 rw-p 00000000 00:00 0 2b4060215000-2b4060216000 ---p 00000000 00:00 0 2b4060216000-2b4060456000 rw-p 00000000 00:00 0 2b4060458000-2b4060485000 r-xp 00000000 3bc:92d40 144115224465690832 ./bcbio/anaconda/lib/python2.7/site-packages/numpy/core/scalarmath.so 2b4060485000-2b4060685000 ---p 0002d000 3bc:92d40 144115224465690832 ./bcbio/anaconda/lib/python2.7/site-packages/numpy/core/scalarmath.so 2b4060685000-2b4060687000 rw-p 0002d000 3bc:92d40 144115224465690832 ./bcbio/anaconda/lib/python2.7/site-packages/numpy/core/scalarmath.so 2b4064000000-2b4064021000 rw-p 00000000 00:00 0 2b4064021000-2b4068000000 ---p 00000000 00:00 0 7fff52242000-7fff52258000 rw-p 00000000 00:00 0 [stack] 7fff52350000-7fff52351000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr: __pos (which is 18446744073709551615) > this->size() (which is 0) /bin/bash: line 1: 4446 Done vardict-java -G ./bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -f 0.1 -N 1483FFPE -b "/project/work/bamprep/1483FFPE/1/21_2015-11-05_project-merged-sort-1_62039291_93059007-prep.bam|/project/work/bamprep/1483Germ/1/22_2015-11-05_project-merged-sort-1_62039291_93059007-prep.bam" -c 1 -S 2 -E 3 -g 4 /project/work/vardict/1/batch05-1_62039291_93059007-raw-regions-regionlimit.bed 4447 | testsomatic.R 4448 | var2vcf_paired.pl -M -P 0.9 -m 4.25 -f 0.1 -N "1483FFPE|1483Germ" 4449 | bcftools filter -m '+' -s 'REJECT' -e 'STATUS !~ "._Somatic"' 2> /dev/null 4450 Segmentation fault | ./bcbio/anaconda/bin/py -x 'bcbio.variation.vardict.depth_freq_filter(x, 0, "bwa")' 4451 | sed 's/._Somatic\/Somatic/' 4452 | sed 's/REJECT,Description=".">/REJECT,Description="Not Somatic via VarDict">/' 4453 | ./bcbio/anaconda/bin/py -x 'bcbio.variation.freebayes.call_somatic(x)' 4454 | awk -F' ' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDX]/, "N", $4) } {print}' 4455 | awk -F' ' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' 4456 Aborted | ./bcbio/bin/vcfstreamsort 4457 | bgzip -c > /project/work/vardict/1/tx/tmpEMlNPx/batch05-1_62039291_93059007-raw.vcf.gz ' returned non-zero exit status 134

chapmanb commented 8 years ago

Sorry about the issue. It looks like Python segfaulted for some reason, causing the whole command chain to fail and downstream tools to complain. Is this reproducible if you re-run the analysis? Sorry for the boring "can you try it again" response but sometimes there are one off seg faults that are hard to identify a cause for. If you can reproduce and provide an example file we'd be happy to dig into it more. Hope this helps.

pengxiao78 commented 8 years ago

Yes, it is running now after I tried it again. Thanks!

From: Brad Chapman [mailto:notifications@github.com] Sent: Wednesday, November 18, 2015 3:33 PM To: chapmanb/bcbio-nextgen bcbio-nextgen@noreply.github.com Cc: Xiao, Peng peng.xiao@unmc.edu Subject: Re: [bcbio-nextgen] variant calling error (#1114)

Sorry about the issue. It looks like Python segfaulted for some reason, causing the whole command chain to fail and downstream tools to complain. Is this reproducible if you re-run the analysis? Sorry for the boring "can you try it again" response but sometimes there are one off seg faults that are hard to identify a cause for. If you can reproduce and provide an example file we'd be happy to dig into it more. Hope this helps.

— Reply to this email directly or view it on GitHubhttps://github.com/chapmanb/bcbio-nextgen/issues/1114#issuecomment-157871329.

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