.command.err - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (HCC1395_tumor_vs_HCC1395_BL;chr21_5117003-5117331.bed)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/8820036da90786c90e718f288a6433/.command.err
Size: 16.8 KB
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (HCC1395_tumor_vs_HCC1395_BL;chr21_5117003-5117331.bed)
Attempt
Content

[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXvb7PFk/chr21_5117003-5117331.bed.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXvb7PFk/chr21_5117003-5117331.bed.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXvb7PFk/chr21_5117003-5117331.bed.gz.tbi
[2026-05-28T23:03:01.498298Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Initiating pyFlow run
[2026-05-28T23:03:01.502116Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaSomaticWorkflow
[2026-05-28T23:03:01.502139Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-05-28T23:03:01.502145Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-05-28T23:03:01.502149Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXvb7PFk'
[2026-05-28T23:03:01.502154Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/strelka/runWorkflow.py -m local -j 8'
[2026-05-28T23:03:01.502159Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] [RunParameters] mode: local
[2026-05-28T23:03:01.502163Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] [RunParameters] nCores: 8
[2026-05-28T23:03:01.502167Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] [RunParameters] memMb: 386708
[2026-05-28T23:03:01.502171Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/strelka/workspace/pyflow.data
[2026-05-28T23:03:01.502175Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-05-28T23:03:01.502179Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-05-28T23:03:01.502183Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-05-28T23:03:01.502187Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-05-28T23:03:01.502742Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-05-28T23:03:01.502851Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [StrelkaSomaticWorkflow] Initiating Strelka somatic workflow version: 2.9.10
[2026-05-28T23:03:01.508430Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2026-05-28T23:03:01.509124Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2026-05-28T23:03:01.509230Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-05-28T23:03:01.509625Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2026-05-28T23:03:01.509841Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2026-05-28T23:03:01.511154Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-05-28T23:03:01.511358Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2026-05-28T23:03:01.511450Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-05-28T23:03:01.511545Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-05-28T23:03:01.511986Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-05-28T23:03:01.512492Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-05-28T23:03:01.513944Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-05-28T23:03:01.514105Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-05-28T23:03:01.514223Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2026-05-28T23:03:01.527895Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-05-28T23:03:01.527982Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-05-28T23:03:01.528050Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2026-05-28T23:03:01.528146Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2026-05-28T23:03:01.528216Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2026-05-28T23:03:01.528289Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2026-05-28T23:03:01.528352Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2026-05-28T23:03:01.528433Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2026-05-28T23:03:01.528501Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2026-05-28T23:03:01.528544Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2026-05-28T23:03:01.539412Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:01.539673Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-05-28T23:03:01.540275Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-05-28T23:03:01.540842Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-05-28T23:03:01.542168Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-05-28T23:03:01.542443Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0000] Task initiated on local node
[2026-05-28T23:03:01.545499Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0001] Task initiated on local node
[2026-05-28T23:03:01.546921Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0003] Task initiated on local node
[2026-05-28T23:03:01.547983Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0002] Task initiated on local node
[2026-05-28T23:03:01.656339Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:01.656631Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-05-28T23:03:01.659204Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0003] Task initiated on local node
[2026-05-28T23:03:01.689009Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.306167Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.306519Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Launching command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.308912Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskRunner:CallGenome+fixVcfHeader_chromId_020_chr21_0000] Task initiated on local node
[2026-05-28T23:03:03.370735Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Completed command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.371023Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.373269Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0000] Task initiated on local node
[2026-05-28T23:03:03.403134Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.918121Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.918446Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.920910Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0001] Task initiated on local node
[2026-05-28T23:03:03.950614Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:15.268250Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:15.268637Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-05-28T23:03:15.270890Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0002] Task initiated on local node
[2026-05-28T23:03:15.333594Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:15.333745Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:15.333860Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2026-05-28T23:03:15.334753Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Launching command task: 'CallGenome+Indel_concat_vcf' from sub-workflow 'CallGenome'
[2026-05-28T23:03:15.336318Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Launching command task: 'CallGenome+SNV_concat_vcf' from sub-workflow 'CallGenome'
[2026-05-28T23:03:15.336474Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2026-05-28T23:03:15.338288Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskRunner:CallGenome+Indel_concat_vcf] Task initiated on local node
[2026-05-28T23:03:15.340084Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskRunner:CallGenome+SNV_concat_vcf] Task initiated on local node
[2026-05-28T23:03:15.369860Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:15.371109Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Completed command task: 'CallGenome+SNV_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:15.371640Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Launching command task: 'CallGenome+SNV_index_vcf' from sub-workflow 'CallGenome'
[2026-05-28T23:03:15.372246Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Completed command task: 'CallGenome+Indel_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:15.372618Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Launching command task: 'CallGenome+Indel_index_vcf' from sub-workflow 'CallGenome'
[2026-05-28T23:03:15.374383Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskRunner:CallGenome+SNV_index_vcf] Task initiated on local node
[2026-05-28T23:03:15.375168Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskRunner:CallGenome+Indel_index_vcf] Task initiated on local node
[2026-05-28T23:03:15.405034Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Completed command task: 'CallGenome+SNV_index_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:15.405085Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Completed command task: 'CallGenome+Indel_index_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:15.405226Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2026-05-28T23:03:15.407323Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2026-05-28T23:03:15.437089Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:20.412209Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2026-05-28T23:03:34.620995Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Strelka somatic workflow successfully completed.
[2026-05-28T23:03:34.620995Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] 
[2026-05-28T23:03:34.620995Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] 	workflow version: 2.9.10
[2026-05-28T23:03:34.621090Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] 
[2026-05-28T23:03:34.621098Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-05-28T23:03:34.621104Z] [nf-e78820036da90786c90e718f288a6433-dbfd3-cmgpq] [678_1] [WorkflowRunner] Elapsed time for full workflow: 33 sec