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Illumina / strelka

Strelka2 germline and somatic small variant caller
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Error in running strelka #199

Open WengangXbio opened 3 years ago

WengangXbio commented 3 years ago

HI developers, Thank you very much for your powerful tool. I have run 1000+ data using sk2 to date. Recently, I came across an error report when I used the same pipeline to run some samples. There are many error lines in log file, but started as follow, ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ [2021-08-27T22:41:58.643644Z] [node3g03.ecdf.ed.ac.uk] [277598_1] [TaskManager] [ERROR] Failed to complete command task: 'EstimateSeqErrorParams+Sample000+countErrors_chromId_021_chr22_0030' launched from sub-workflow 'EstimateSeqErrorParams+Sample000', error code: 1, command: '/home/s1874451/schoenebeck_group/WENGANG/anaconda_env/strelka/share/strelka-2.9.10-0/libexec/GetSequenceAlleleCounts --region chr22:58225294-60166136 --ref /home/s1874451/schoenebeck_group/WENGANG/Liuyang_cnv/ROS_Cfam/ROS_Cfam1.fa --max-indel-size 49 --counts-file /exports/eddie/scratch/s1874451/sk2_male/5.sk2/sk2_SAMC010560/workspace/errorEstimation.tmpdir/sequenceAlleleCounts.Sample000.chromId_021_chr22_0030.bin --nonempty-site-count-file /exports/eddie/scratch/s1874451/sk2_male/5.sk2/sk2_SAMC010560/workspace/errorEstimation.tmpdir/nonEmptySiteCounts.Sample000.chromId_021_chr22_0030.tsv --align-file /exports/eddie/scratch/s1874451/sk2_male/SAMC010560.sorted.bam --chrom-depth-file /exports/eddie/scratch/s1874451/sk2_male/5.sk2/sk2_SAMC010560/workspace/chromDepth.tsv' [2021-08-27T22:41:58.655934Z] [node3g03.ecdf.ed.ac.uk] [277598_1] [TaskManager] [ERROR] [EstimateSeqErrorParams+Sample000+countErrors_chromId_021_chr22_0030] Error Message: [2021-08-27T22:41:58.661012Z] [node3g03.ecdf.ed.ac.uk] [277598_1] [TaskManager] [ERROR] [EstimateSeqErrorParams+Sample000+countErrors_chromId_021_chr22_0030] Last 14 stderr lines from task (of 14 total lines): ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ The full report is attached below. rerun_sk2.e14053796.txt It would be great if you can help me out. Best wishes, Wengang

bcantarel commented 2 years ago

I think I am getting the same error -- just running it on public NA12878 data for workflow testing:

[2022-04-23T00:01:17.022656Z] [530311a99f50] [7705_1] [TaskManager] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow' [2022-04-23T00:01:22.934456Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors: [2022-04-23T00:01:22.939565Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow' [2022-04-23T00:01:22.943819Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr1_0001' launched from sub-workflow 'CallGenome', error code: 1, command: '/usr/local/libexec/starling2 --region chr1:11855069-23710136 --ref /data/giab/dnaref/genome.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /data/giab/strelka/workspace/genomeSegment.tmpdir/segment.chromId_000_chr1_0001. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /data/giab/strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0001.xml --align-file /data/giab/NA12878.primary.bam --gvcf-skip-header --indel-error-models-file /usr/local/share/config/indelErrorModel.json --theta-file /usr/local/share/config/theta.json' [2022-04-23T00:01:22.948752Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] Error Message: [2022-04-23T00:01:22.953411Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] Anomalous task wrapper stderr output. Wrapper signal file: '/data/giab/strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/005/pyflowTaskWrapper.signal.txt' [2022-04-23T00:01:22.957526Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] Logging 6 line(s) of task wrapper log output below: [2022-04-23T00:01:22.961971Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] [taskWrapper-stderr] [2022-04-23T00:00:49.988583Z] [530311a99f50] [7705_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr1_0001] [wrapperSignal] wrapperStart [2022-04-23T00:01:22.966016Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] [taskWrapper-stderr] [2022-04-23T00:00:49.999119Z] [530311a99f50] [7705_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr1_0001] [wrapperSignal] taskStart [2022-04-23T00:01:22.970959Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] [taskWrapper-stderr] [2022-04-23T00:00:50.372647Z] [530311a99f50] [7705_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr1_0001] [wrapperSignal] taskExitCode -6 [2022-04-23T00:01:22.975747Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] [taskWrapper-stderr] [2022-04-23T00:00:50.378081Z] [530311a99f50] [7705_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr1_0001] [wrapperSignal] taskStderrTail 2 [2022-04-23T00:01:22.979482Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] [taskWrapper-stderr] Last 1 stderr lines from task (of 1 total lines): [2022-04-23T00:01:22.983619Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] [taskWrapper-stderr] [2022-04-23T00:00:50.216249Z] [530311a99f50] [7705_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] starling2: /opt/strelka/src/c++/lib/starling_common/starling_read_align_score.cpp:223: IndelKey getMatchingIndelKey(const CandidateAlignment&, pos_t, unsigned int, unsigned int, const std::pair<unsigned int, unsigned int>&, unsigned int): AssertionisFound' failed. [2022-04-23T00:01:22.987164Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr1_0002' launched from sub-workflow 'CallGenome', error code: 1, command: '/usr/local/libexec/starling2 --region chr1:23710137-35565204 --ref /data/giab/dnaref/genome.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /data/giab/strelka/workspace/genomeSegment.tmpdir/segment.chromId_000_chr1_0002. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /data/giab/strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0002.xml --align-file /data/giab/NA12878.primary.bam --gvcf-skip-header --indel-error-models-file /usr/local/share/config/indelErrorModel.json --theta-file /usr/local/share/config/theta.json' [2022-04-23T00:01:22.991141Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0002] Error Message: [2022-04-23T00:01:22.995338Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0002] Anomalous task wrapper stderr output. Wrapper signal file: '/data/giab/strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/008/pyflowTaskWrapper.signal.txt' [2022-04-23T00:01:22.999722Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0002] Logging 6 line(s) of task wrapper log output below: [2022-04-23T00:01:23.004228Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0002] [taskWrapper-stderr] [2022-04-23T00:00:49.974917Z] [530311a99f50] [7705_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr1_0002] [wrapperSignal] wrapperStart [2022-04-23T00:01:23.008204Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0002] [taskWrapper-stderr] [2022-04-23T00:00:49.988051Z] [530311a99f50] [7705_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr1_0002] [wrapperSignal] taskStart [2022-04-23T00:01:23.012489Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0002] [taskWrapper-stderr] [2022-04-23T00:00:50.535345Z] [530311a99f50] [7705_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr1_0002] [wrapperSignal] taskExitCode -6 [2022-04-23T00:01:23.017062Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0002] [taskWrapper-stderr] [2022-04-23T00:00:50.540586Z] [530311a99f50] [7705_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr1_0002] [wrapperSignal] taskStderrTail 2 [2022-04-23T00:01:23.021544Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0002] [taskWrapper-stderr] Last 1 stderr lines from task (of 1 total lines): [2022-04-23T00:01:23.025957Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0002] [taskWrapper-stderr] [2022-04-23T00:00:50.372550Z] [530311a99f50] [7705_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0002] starling2: /opt/strelka/src/c++/lib/starling_common/starling_read_align_score.cpp:223: IndelKey getMatchingIndelKey(const CandidateAlignment&, pos_t, unsigned int, unsigned int, const std::pair<unsigned int, unsigned int>&, unsigned int): Assertion isFound' failed. [2022-04-23T00:01:23.030007Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr1_0006' launched from sub-workflow 'CallGenome', error code: 1, command: '/usr/local/libexec/starling2 --region chr1:71130409-82985476 --ref /data/giab/dnaref/genome.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /data/giab/strelka/workspace/genomeSegment.tmpdir/segment.chromId_000_chr1_0006. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /data/giab/strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0006.xml --align-file /data/giab/NA12878.primary.bam --gvcf-skip-header --indel-error-models-file /usr/local/share/config/indelErrorModel.json --theta-file /usr/local/share/config/theta.json' [2022-04-23T00:01:23.034362Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0006] Error Message: [2022-04-23T00:01:23.038582Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0006] Anomalous task wrapper stderr output. Wrapper signal file: '/data/giab/strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/020/pyflowTaskWrapper.signal.txt' [2022-04-23T00:01:23.042893Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0006] Logging 6 line(s) of task wrapper log output below: [2022-04-23T00:01:23.046579Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0006] [taskWrapper-stderr] [2022-04-23T00:00:49.963629Z] [530311a99f50] [7705_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr1_0006] [wrapperSignal] wrapperStart [2022-04-23T00:01:23.050657Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0006] [taskWrapper-stderr] [2022-04-23T00:00:49.973566Z] [530311a99f50] [7705_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr1_0006] [wrapperSignal] taskStart [2022-04-23T00:01:23.054419Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0006] [taskWrapper-stderr] [2022-04-23T00:00:50.769983Z] [530311a99f50] [7705_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr1_0006] [wrapperSignal] taskExitCode -6 [2022-04-23T00:01:23.058449Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0006] [taskWrapper-stderr] [2022-04-23T00:00:50.775297Z] [530311a99f50] [7705_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr1_0006] [wrapperSignal] taskStderrTail 2 [2022-04-23T00:01:23.062218Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0006] [taskWrapper-stderr] Last 1 stderr lines from task (of 1 total lines): [2022-04-23T00:01:23.066381Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0006] [taskWrapper-stderr] [2022-04-23T00:00:50.618680Z] [530311a99f50] [7705_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0006] starling2: /opt/strelka/src/c++/lib/starling_common/starling_read_align_score.cpp:223: IndelKey getMatchingIndelKey(const CandidateAlignment&, pos_t, unsigned int, unsigned int, const std::pair<unsigned int, unsigned int>&, unsigned int): AssertionisFound' failed. [2022-04-23T00:01:23.070858Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr1_0005' launched from sub-workflow 'CallGenome', error code: 1, command: '/usr/local/libexec/starling2 --region chr1:59275341-71130408 --ref /data/giab/dnaref/genome.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /data/giab/strelka/workspace/genomeSegment.tmpdir/segment.chromId_000_chr1_0005. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /data/giab/strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0005.xml --align-file /data/giab/NA12878.primary.bam --gvcf-skip-header --indel-error-models-file /usr/local/share/config/indelErrorModel.json --theta-file /usr/local/share/config/theta.json' [2022-04-23T00:01:23.075036Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0005] Error Message: [2022-04-23T00:01:23.079580Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0005] Anomalous task wrapper stderr output. Wrapper signal file: '/data/giab/strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/017/pyflowTaskWrapper.signal.txt' [2022-04-23T00:01:23.083983Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0005] Logging 6 line(s) of task wrapper log output below: [2022-04-23T00:01:23.087914Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0005] [taskWrapper-stderr] [2022-04-23T00:00:49.954498Z] [530311a99f50] [7705_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr1_0005] [wrapperSignal] wrapperStart [2022-04-23T00:01:23.092446Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0005] [taskWrapper-stderr] [2022-04-23T00:00:49.966350Z] [530311a99f50] [7705_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr1_0005] [wrapperSignal] taskStart [2022-04-23T00:01:23.096484Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0005] [taskWrapper-stderr] [2022-04-23T00:00:50.637593Z] [530311a99f50] [7705_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr1_0005] [wrapperSignal] taskExitCode -6 [2022-04-23T00:01:23.100648Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0005] [taskWrapper-stderr] [2022-04-23T00:00:50.645223Z] [530311a99f50] [7705_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr1_0005] [wrapperSignal] taskStderrTail 2 [2022-04-23T00:01:23.105069Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0005] [taskWrapper-stderr] Last 1 stderr lines from task (of 1 total lines): [2022-04-23T00:01:23.109267Z] [530311a99f50] [7705_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0005] [taskWrapper-stderr] [2022-04-23T00:00:50.477435Z] [530311a99f50] [7705_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0005] starling2: /opt/strelka/src/c++/lib/starling_common/starling_read_align_score.cpp:223: IndelKey getMatchingIndelKey(const CandidateAlignment&, pos_t, unsigned int, unsigned int, const std::pair<unsigned int, unsigned int>&, unsigned int): Assertion isFound' failed.