nf-core
nf-test failing for strelka/somatic
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Description of the bug
strelka/somatic failed the nf-test using conda, raising a fail check for https://github.com/nf-core/modules/pull/7978
Below is the error message.
`Test Subworkflow BAM_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING_STRELKA
Test [99a48627] 'human - cram - paired_end'
> Nextflow 24.10.5 is available - Please consider updating your version to it
> N E X T F L O W ~ version 24.10.2
> Launching /home/runner/_work/modules/modules/.nf-test-99a486272882e857e951cd9ea482b82d.nf [fervent_legentil] DSL2 - revision: eee2d239d3
> Creating env using conda: /home/runner/_work/modules/modules/subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_strelka/tests/../../../../modules/nf-core/strelka/somatic/environment.yml [cache /home/runner/_work/modules/modules/.nf-test/tests/99a486272882e857e951cd9ea482b82d/work/conda/env-d678b8a4ce4a536e-0512a6ec334e8ec270675e08f9ccf18d]
> [2c/f5918b] Submitted process > BAM_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING_STRELKA:STRELKA_SOMATIC (test)
> ERROR ~ Error executing process > 'BAM_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING_STRELKA:STRELKA_SOMATIC (test)'
>
> Caused by:
> Process BAM_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING_STRELKA:STRELKA_SOMATIC (test) terminated with an error exit status (1)
>
>
> Command executed:
>
> configureStrelkaSomaticWorkflow.py
> --tumor test2.paired_end.recalibrated.sorted.cram
> --normal test.paired_end.recalibrated.sorted.cram
> --referenceFasta genome.fasta
> --callRegions multi_intervals.bed.gz
>
>
> --runDir strelka
>
> sed -i s/"isEmail = isLocalSmtp()"/"isEmail = False"/g strelka/runWorkflow.py
>
> python strelka/runWorkflow.py -m local -j 2
> mv strelka/results/variants/somatic.indels.vcf.gz test.somatic_indels.vcf.gz
> mv strelka/results/variants/somatic.indels.vcf.gz.tbi test.somatic_indels.vcf.gz.tbi
> mv strelka/results/variants/somatic.snvs.vcf.gz test.somatic_snvs.vcf.gz
> mv strelka/results/variants/somatic.snvs.vcf.gz.tbi test.somatic_snvs.vcf.gz.tbi
>
> cat <<-END_VERSIONS > versions.yml
> "BAM_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING_STRELKA:STRELKA_SOMATIC":
> strelka: $( configureStrelkaSomaticWorkflow.py --version )
> END_VERSIONS
>
> Command exit status:
> 1
>
> Command output:
>
> Successfully created workflow run script.
> To execute the workflow, run the following script and set appropriate options:
>
> strelka/runWorkflow.py
>
> Command error:
> [2025-03-24T19:11:26.600908Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
> [2025-03-24T19:11:26.600990Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
> [2025-03-24T19:11:26.601229Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
> [2025-03-24T19:11:26.601434Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
> [2025-03-24T19:11:26.666160Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
> [2025-03-24T19:11:26.666231Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] Completed command task: 'getChromDepth_removeTmpDir' launched from master workflow
> [2025-03-24T19:11:26.666529Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0000' from sub-workflow 'CallGenome'
> [2025-03-24T19:11:26.666699Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0003' from sub-workflow 'CallGenome'
> [2025-03-24T19:11:26.670044Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_000_chr21_0000] Task initiated on local node
> [2025-03-24T19:11:26.671186Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_000_chr21_0003] Task initiated on local node
Error: [2025-03-24T19:11:26.831074Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0003' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/_work/modules/modules/.nf-test/tests/99a486272882e857e951cd9ea482b82d/work/conda/env-d678b8a4ce4a536e-0512a6ec334e8ec270675e08f9ccf18d/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:35032489-46709983 --ref genome.fasta --max-indel-size 49 --call-regions-bed multi_intervals.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/runner/_work/modules/modules/.nf-test/tests/99a486272882e857e951cd9ea482b82d/work/conda/env-d678b8a4ce4a536e-0512a6ec334e8ec270675e08f9ccf18d/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/_work/modules/modules/.nf-test/tests/99a486272882e857e951cd9ea482b82d/work/conda/env-d678b8a4ce4a536e-0512a6ec334e8ec270675e08f9ccf18d/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.paired_end.recalibrated.sorted.cram --tumor-align-file test2.paired_end.recalibrated.sorted.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr21_0003.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr21_0003.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr21_0003.xml --strelka-skip-header --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
Error: [2025-03-24T19:11:26.831150Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Error Message:
Error: [2025-03-24T19:11:26.831161Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/015/pyflowTaskWrapper.signal.txt'
Error: [2025-03-24T19:11:26.831171Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Logging 5 line(s) of task wrapper log output below:
Error: [2025-03-24T19:11:26.831181Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-03-24T19:11:26.682847Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] wrapperStart
Error: [2025-03-24T19:11:26.831211Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-03-24T19:11:26.691395Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskStart
Error: [2025-03-24T19:11:26.831225Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-03-24T19:11:26.798849Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskExitCode -11
Error: [2025-03-24T19:11:26.831236Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-03-24T19:11:26.805771Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskStderrTail 1
Error: [2025-03-24T19:11:26.831246Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
Error: [2025-03-24T19:11:26.831257Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
Error: [2025-03-24T19:11:26.831312Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0000' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/_work/modules/modules/.nf-test/tests/99a486272882e857e951cd9ea482b82d/work/conda/env-d678b8a4ce4a536e-0512a6ec334e8ec270675e08f9ccf18d/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:1-11677496 --ref genome.fasta --max-indel-size 49 --call-regions-bed multi_intervals.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/runner/_work/modules/modules/.nf-test/tests/99a486272882e857e951cd9ea482b82d/work/conda/env-d678b8a4ce4a536e-0512a6ec334e8ec270675e08f9ccf18d/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/_work/modules/modules/.nf-test/tests/99a486272882e857e951cd9ea482b82d/work/conda/env-d678b8a4ce4a536e-0512a6ec334e8ec270675e08f9ccf18d/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.paired_end.recalibrated.sorted.cram --tumor-align-file test2.paired_end.recalibrated.sorted.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr21_0000.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr21_0000.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr21_0000.xml --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
Error: [2025-03-24T19:11:26.831335Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Error Message:
Error: [2025-03-24T19:11:26.831344Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/008/pyflowTaskWrapper.signal.txt'
Error: [2025-03-24T19:11:26.831353Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Logging 5 line(s) of task wrapper log output below:
Error: [2025-03-24T19:11:26.831361Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-03-24T19:11:26.682806Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] wrapperStart
Error: [2025-03-24T19:11:26.831370Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-03-24T19:11:26.689635Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStart
Error: [2025-03-24T19:11:26.831379Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-03-24T19:11:26.798872Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskExitCode -11
Error: [2025-03-24T19:11:26.831388Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-03-24T19:11:26.805772Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStderrTail 1
Error: [2025-03-24T19:11:26.831396Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
Error: [2025-03-24T19:11:27.646327Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [TaskManager] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'
Error: [2025-03-24T19:11:35.138535Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
Error: [2025-03-24T19:11:35.138604Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0000' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/_work/modules/modules/.nf-test/tests/99a486272882e857e951cd9ea482b82d/work/conda/env-d678b8a4ce4a536e-0512a6ec334e8ec270675e08f9ccf18d/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:1-11677496 --ref genome.fasta --max-indel-size 49 --call-regions-bed multi_intervals.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/runner/_work/modules/modules/.nf-test/tests/99a486272882e857e951cd9ea482b82d/work/conda/env-d678b8a4ce4a536e-0512a6ec334e8ec270675e08f9ccf18d/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/_work/modules/modules/.nf-test/tests/99a486272882e857e951cd9ea482b82d/work/conda/env-d678b8a4ce4a536e-0512a6ec334e8ec270675e08f9ccf18d/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.paired_end.recalibrated.sorted.cram --tumor-align-file test2.paired_end.recalibrated.sorted.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr21_0000.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr21_0000.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr21_0000.xml --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
Error: [2025-03-24T19:11:35.138643Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Error Message:
Error: [2025-03-24T19:11:35.138651Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/008/pyflowTaskWrapper.signal.txt'
Error: [2025-03-24T19:11:35.138664Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Logging 5 line(s) of task wrapper log output below:
Error: [2025-03-24T19:11:35.138674Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-03-24T19:11:26.682806Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] wrapperStart
Error: [2025-03-24T19:11:35.138683Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-03-24T19:11:26.689635Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStart
Error: [2025-03-24T19:11:35.138693Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-03-24T19:11:26.798872Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskExitCode -11
Error: [2025-03-24T19:11:35.138705Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-03-24T19:11:26.805772Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStderrTail 1
Error: [2025-03-24T19:11:35.138719Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
Error: [2025-03-24T19:11:35.138727Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0003' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/_work/modules/modules/.nf-test/tests/99a486272882e857e951cd9ea482b82d/work/conda/env-d678b8a4ce4a536e-0512a6ec334e8ec270675e08f9ccf18d/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:35032489-46709983 --ref genome.fasta --max-indel-size 49 --call-regions-bed multi_intervals.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/runner/_work/modules/modules/.nf-test/tests/99a486272882e857e951cd9ea482b82d/work/conda/env-d678b8a4ce4a536e-0512a6ec334e8ec270675e08f9ccf18d/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/_work/modules/modules/.nf-test/tests/99a486272882e857e951cd9ea482b82d/work/conda/env-d678b8a4ce4a536e-0512a6ec334e8ec270675e08f9ccf18d/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.paired_end.recalibrated.sorted.cram --tumor-align-file test2.paired_end.recalibrated.sorted.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr21_0003.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr21_0003.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr21_0003.xml --strelka-skip-header --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
Error: [2025-03-24T19:11:35.138745Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Error Message:
Error: [2025-03-24T19:11:35.138758Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/015/pyflowTaskWrapper.signal.txt'
Error: [2025-03-24T19:11:35.138772Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Logging 5 line(s) of task wrapper log output below:
Error: [2025-03-24T19:11:35.138781Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-03-24T19:11:26.682847Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] wrapperStart
Error: [2025-03-24T19:11:35.138789Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-03-24T19:11:26.691395Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskStart
Error: [2025-03-24T19:11:35.138797Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-03-24T19:11:26.798849Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskExitCode -11
Error: [2025-03-24T19:11:35.138806Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-03-24T19:11:26.805771Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskStderrTail 1
Error: [2025-03-24T19:11:35.138815Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
Error: [2025-03-24T19:11:35.138823Z] [ip-10-1-45-35.eu-west-1.compute.internal] [10039_1] [WorkflowRunner] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'
>
> Work dir:
> /home/runner/_work/modules/modules/.nf-test/tests/99a486272882e857e951cd9ea482b82d/work/2c/f5918bd69887458361053824e709d8
>
> Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh
>
> -- Check '/home/runner/_work/modules/modules/.nf-test/tests/99a486272882e857e951cd9ea482b82d/meta/nextflow.log' file for details
Assertion failed:
assert workflow.success | | workflow false
java.lang.RuntimeException: Different Snapshot: [ [ { { "0": [ "0": [
], ],
"1": [ "1": [
"versions.yml:md5,d80432f72767d21f7050a310e8dbfd6e" |
], ],
"vcf": [ "vcf": [
], ],
"versions": [ "versions": [
"versions.yml:md5,d80432f72767d21f7050a310e8dbfd6e" |
] ]
} }
] ]
FAILED (25.522s)`
Command used and terminal output
Relevant files
No response
System information
No response
