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Illumina / strelka

Strelka2 germline and somatic small variant caller
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strelka2 Assertion `! indelRates.isInit' failed #211

Closed sagitaninta closed 2 years ago

sagitaninta commented 2 years ago

I have run the following call for 67 samples:

python ~/software/strelka-2.9.2.centos6_x86_64/bin/configureStrelkaGermlineWorkflow.py \
    --bam RD100_mdup.bam \
        --bam RD101_mdup.bam \
        --bam RD102_mdup.bam \
        --bam ... (and so on until the 67th)
        --referenceFasta /data/shared/REF/TAURUS/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa \
    --callRegions Bos_taurus.ARS-UCD1.2.noContig.bed.gz \
    --runDir anoa_all/

And the job failed with the following message in 

cat anoa_all/workflow.exitcode.txt 
1
cat anoa_all/workflow.error.log.txt 
[2022-04-02T11:46:38.834295Z] [gobekli] [132439_1] [TaskManager] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_1_0000' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/btx638/software/strelka-2.9.2.centos6_x86_64/libexec/starling2 --region 1:1-11323865 --ref /data/shared/REF/TAURUS/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa --max-indel-size 49 --call-regions-bed /data/btx638/strelka_2022-04-02/Bos_taurus.ARS-UCD1.2.noContig.bed.gz --min-mapping-quality 20 --gvcf-output-prefix /data/btx638/strelka_2022-04-02/anoa_all/workspace/genomeSegment.tmpdir/segment.chromId_000_1_0000. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /data/btx638/strelka_2022-04-02/anoa_all/workspace/genomeSegment.tmpdir/runStats.chromId_000_1_0000.xml --snv-scoring-model-file /home/btx638/software/strelka-2.9.2.centos6_x86_64/share/config/germlineSNVScoringModels.json --indel-scoring-model-file /home/btx638/software/strelka-2.9.2.centos6_x86_64/share/config/germlineIndelScoringModels.json --align-file /data/btx638/strelka_2022-04-02/RD100_mdup.bam --align-file /data/btx638/strelka_2022-04-02/RD101_mdup.bam --align-file /data/btx638/strelka_2022-04-02/RD102_mdup.bam 
... (all bam files under --align-file until the 67th bam)  
--chrom-depth-file /data/btx638/strelka_2022-04-02/anoa_all/workspace/chromDepth.tsv --indel-error-models-file /data/btx638/strelka_2022-04-02/anoa_all/workspace/sequenceErrorModel.Sample000.json --indel-error-models-file /data/btx638/strelka_2022-04-02/anoa_all/workspace/sequenceErrorModel.Sample001.json 
... (all indel-error-models-file until the 67th sample)
--theta-file /home/btx638/software/strelka-2.9.2.centos6_x86_64/share/config/theta.json
[2022-04-02T11:46:38.851656Z] [gobekli] [132439_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_1_0000] Error Message:
[2022-04-02T11:46:38.888112Z] [gobekli] [132439_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_1_0000] Anomalous task wrapper stderr output. Wrapper signal file: '/data/btx638/strelka_2022-04-02/anoa_all/workspace/pyflow.data/logs/tmp/taskWrapperLogs/009/221/pyflowTaskWrapper.signal.txt'
[2022-04-02T11:46:38.893203Z] [gobekli] [132439_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_1_0000] Logging 6 line(s) of task wrapper log output below:
[2022-04-02T11:46:38.896072Z] [gobekli] [132439_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_1_0000] [taskWrapper-stderr] [2022-04-02T11:46:38.551910Z] [gobekli] [132439_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_1_0000] [wrapperSignal] wrapperStart
[2022-04-02T11:46:38.898189Z] [gobekli] [132439_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_1_0000] [taskWrapper-stderr] [2022-04-02T11:46:38.586420Z] [gobekli] [132439_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_1_0000] [wrapperSignal] taskStart
[2022-04-02T11:46:38.900375Z] [gobekli] [132439_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_1_0000] [taskWrapper-stderr] [2022-04-02T11:46:38.781035Z] [gobekli] [132439_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_1_0000] [wrapperSignal] taskExitCode -6
[2022-04-02T11:46:38.908544Z] [gobekli] [132439_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_1_0000] [taskWrapper-stderr] [2022-04-02T11:46:38.813002Z] [gobekli] [132439_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_1_0000] [wrapperSignal] taskStderrTail 2
[2022-04-02T11:46:38.910797Z] [gobekli] [132439_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_1_0000] [taskWrapper-stderr] Last 1 stderr lines from task (of 1 total lines):
[2022-04-02T11:46:38.913126Z] [gobekli] [132439_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_1_0000] [taskWrapper-stderr] [2022-04-02T11:46:38.624735Z] [gobekli] [132439_1] [CallGenome+callGenomeSegment_chromId_000_1_0000] starling2: /builder/src/c++/lib/calibration/IndelErrorRateSet.hh:138: void IndelErrorRateSet::addRate(unsigned int, unsigned int, double, double, double): Assertion `! indelRates.isInit' failed.
[2022-04-02T11:46:38.915232Z] [gobekli] [132439_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
[2022-04-02T12:15:08.328037Z] [gobekli] [132439_1] [TaskManager] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'
[2022-04-02T12:15:21.022713Z] [gobekli] [132439_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
[2022-04-02T12:15:21.037336Z] [gobekli] [132439_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_1_0000' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/btx638/software/strelka-2.9.2.centos6_x86_64/libexec/starling2 --region 1:1-11323865 --ref /data/shared/REF/TAURUS/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa --max-indel-size 49 --call-regions-bed /data/btx638/strelka_2022-04-02/Bos_taurus.ARS-UCD1.2.noContig.bed.gz --min-mapping-quality 20 --gvcf-output-prefix /data/btx638/strelka_2022-04-02/anoa_all/workspace/genomeSegment.tmpdir/segment.chromId_000_1_0000. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /data/btx638/strelka_2022-04-02/anoa_all/workspace/genomeSegment.tmpdir/runStats.chromId_000_1_0000.xml --snv-scoring-model-file /home/btx638/software/strelka-2.9.2.centos6_x86_64/share/config/germlineSNVScoringModels.json --indel-scoring-model-file /home/btx638/software/strelka-2.9.2.centos6_x86_64/share/config/germlineIndelScoringModels.json --align-file /data/btx638/strelka_2022-04-02/RD100_mdup.bam --align-file /data/btx638/strelka_2022-04-02/RD101_mdup.bam --align-file /data/btx638/strelka_2022-04-02/RD102_mdup.bam ... (then the remaining same as above)

head anoa_all/workflow.warning.log.txt 
[2022-04-02T11:46:37.620677Z] [gobekli] [132439_1] [StrelkaGermlineWorkflow] [WARNING] Adaptive indel error rate estimation for sample 'default' did not succeed, using static indel error model instead.
[2022-04-02T11:46:37.712776Z] [gobekli] [132439_1] [StrelkaGermlineWorkflow] [WARNING] Adaptive indel error rate estimation for sample 'default' did not succeed, using static indel error model instead.
[2022-04-02T11:46:37.742533Z] [gobekli] [132439_1] [StrelkaGermlineWorkflow] [WARNING] Adaptive indel error rate estimation for sample 'default' did not succeed, using static indel error model instead.
[2022-04-02T11:46:37.746967Z] [gobekli] [132439_1] [StrelkaGermlineWorkflow] [WARNING] Adaptive indel error rate estimation for sample 'default' did not succeed, using static indel error model instead.
[2022-04-02T11:46:37.750391Z] [gobekli] [132439_1] [StrelkaGermlineWorkflow] [WARNING] Adaptive indel error rate estimation for sample 'default' did not succeed, using static indel error model instead.
[2022-04-02T11:46:37.753759Z] [gobekli] [132439_1] [StrelkaGermlineWorkflow] [WARNING] Adaptive indel error rate estimation for sample 'default' did not succeed, using static indel error model instead.
[2022-04-02T11:46:37.757041Z] [gobekli] [132439_1] [StrelkaGermlineWorkflow] [WARNING] Adaptive indel error rate estimation for sample 'default' did not succeed, using static indel error model instead.
[2022-04-02T11:46:37.760327Z] [gobekli] [132439_1] [StrelkaGermlineWorkflow] [WARNING] Adaptive indel error rate estimation for sample 'default' did not succeed, using static indel error model instead.
[2022-04-02T11:46:37.763865Z] [gobekli] [132439_1] [StrelkaGermlineWorkflow] [WARNING] Adaptive indel error rate estimation for sample 'default' did not succeed, using static indel error model instead.
[2022-04-02T11:46:37.782328Z] [gobekli] [132439_1] [StrelkaGermlineWorkflow] [WARNING] Adaptive indel error rate estimation for sample 'default' did not succeed, using static indel error model instead.

The same samples have no problem being ran as singles, I can get the .vcf and .g.vcf of all 67 samples, but it throws this error when I try to call them as multiple and I suspect that [CallGenome+callGenomeSegment_chromId_000_1_0000] starling2: /builder/src/c++/lib/calibration/IndelErrorRateSet.hh:138: void IndelErrorRateSet::addRate(unsigned int, unsigned int, double, double, double): Assertion '! indelRates.isInit' failed. is the main cause, considering the warning log also.

I have followed the error message Anomalous task wrapper stderr output. Wrapper signal file: '/data/btx638/strelka_2022-04-02/anoa_all/workspace/pyflow.data/logs/tmp/taskWrapperLogs/009/221/pyflowTaskWrapper.signal.txt' and this is what I found:

cat /data/btx638/strelka_2022-04-02/anoa_all/workspace/pyflow.data/logs/tmp/taskWrapperLogs/009/221/pyflowTaskWrapper.signal.txt
[2022-04-02T11:46:38.551910Z] [gobekli] [132439_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_1_0000] [wrapperSignal] wrapperStart
[2022-04-02T11:46:38.586420Z] [gobekli] [132439_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_1_0000] [wrapperSignal] taskStart
[2022-04-02T11:46:38.781035Z] [gobekli] [132439_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_1_0000] [wrapperSignal] taskExitCode -6
[2022-04-02T11:46:38.813002Z] [gobekli] [132439_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_1_0000] [wrapperSignal] taskStderrTail 2
Last 1 stderr lines from task (of 1 total lines):
[2022-04-02T11:46:38.624735Z] [gobekli] [132439_1] [CallGenome+callGenomeSegment_chromId_000_1_0000] starling2: /builder/src/c++/lib/calibration/IndelErrorRateSet.hh:138: void IndelErrorRateSet::addRate(unsigned int, unsigned int, double, double, double): Assertion `! indelRates.isInit' failed.

Can anyone tell me what can I try to solve this? Removing low-coverage genomes does not help

sagitaninta commented 2 years ago

I have updated my strelka to the latest one, 2.9.10, and I got the problem solved.