.command.err - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (HCC1395_tumor_vs_HCC1395_BL;chr21_44102678-44103072.bed)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/13d2fa860f2962f35958befd8263c4/.command.err
Size: 16.5 KB
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (HCC1395_tumor_vs_HCC1395_BL;chr21_44102678-44103072.bed)
Attempt
Content

[2026-05-28T23:03:00.643605Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Initiating pyFlow run
[2026-05-28T23:03:00.644833Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaSomaticWorkflow
[2026-05-28T23:03:00.644859Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-05-28T23:03:00.644865Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-05-28T23:03:00.644869Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXX0A63pb'
[2026-05-28T23:03:00.644873Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/strelka/runWorkflow.py -m local -j 8'
[2026-05-28T23:03:00.644879Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] [RunParameters] mode: local
[2026-05-28T23:03:00.644883Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] [RunParameters] nCores: 8
[2026-05-28T23:03:00.644887Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] [RunParameters] memMb: 386708
[2026-05-28T23:03:00.644891Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/strelka/workspace/pyflow.data
[2026-05-28T23:03:00.644895Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-05-28T23:03:00.644899Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-05-28T23:03:00.644903Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-05-28T23:03:00.644907Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-05-28T23:03:00.645921Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-05-28T23:03:00.645980Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [StrelkaSomaticWorkflow] Initiating Strelka somatic workflow version: 2.9.10
[2026-05-28T23:03:00.651599Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2026-05-28T23:03:00.652356Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2026-05-28T23:03:00.652691Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2026-05-28T23:03:00.652895Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2026-05-28T23:03:00.653926Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-05-28T23:03:00.654601Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2026-05-28T23:03:00.654732Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-05-28T23:03:00.654877Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-05-28T23:03:00.654989Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-05-28T23:03:00.655641Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-05-28T23:03:00.655938Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-05-28T23:03:00.657298Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-05-28T23:03:00.657746Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2026-05-28T23:03:00.657953Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-05-28T23:03:00.670198Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-05-28T23:03:00.670311Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-05-28T23:03:00.670378Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2026-05-28T23:03:00.670464Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2026-05-28T23:03:00.670533Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2026-05-28T23:03:00.670625Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2026-05-28T23:03:00.670692Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2026-05-28T23:03:00.670770Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2026-05-28T23:03:00.670871Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2026-05-28T23:03:00.670914Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2026-05-28T23:03:00.681596Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:00.681821Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-05-28T23:03:00.682530Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-05-28T23:03:00.683171Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-05-28T23:03:00.685356Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0002] Task initiated on local node
[2026-05-28T23:03:00.685928Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-05-28T23:03:00.686208Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0000] Task initiated on local node
[2026-05-28T23:03:00.689029Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0001] Task initiated on local node
[2026-05-28T23:03:00.690299Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0003] Task initiated on local node
[2026-05-28T23:03:00.750358Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:00.750659Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-05-28T23:03:00.752573Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:00.752976Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Launching command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-05-28T23:03:00.753425Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0001] Task initiated on local node
[2026-05-28T23:03:00.753907Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:00.755396Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-05-28T23:03:00.755937Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskRunner:CallGenome+fixVcfHeader_chromId_020_chr21_0000] Task initiated on local node
[2026-05-28T23:03:00.757695Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0002] Task initiated on local node
[2026-05-28T23:03:00.788544Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:00.788620Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:00.804205Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Completed command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:00.804467Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-05-28T23:03:00.806631Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0000] Task initiated on local node
[2026-05-28T23:03:00.868862Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:13.989300Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:13.989650Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-05-28T23:03:13.992402Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0003] Task initiated on local node
[2026-05-28T23:03:14.021822Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:14.021971Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:14.022084Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2026-05-28T23:03:14.022493Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Launching command task: 'CallGenome+Indel_concat_vcf' from sub-workflow 'CallGenome'
[2026-05-28T23:03:14.022901Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Launching command task: 'CallGenome+SNV_concat_vcf' from sub-workflow 'CallGenome'
[2026-05-28T23:03:14.025532Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2026-05-28T23:03:14.026877Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskRunner:CallGenome+Indel_concat_vcf] Task initiated on local node
[2026-05-28T23:03:14.027684Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskRunner:CallGenome+SNV_concat_vcf] Task initiated on local node
[2026-05-28T23:03:14.056162Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Completed command task: 'CallGenome+Indel_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:14.056230Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:14.056250Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Completed command task: 'CallGenome+SNV_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:14.056427Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Launching command task: 'CallGenome+SNV_index_vcf' from sub-workflow 'CallGenome'
[2026-05-28T23:03:14.056964Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Launching command task: 'CallGenome+Indel_index_vcf' from sub-workflow 'CallGenome'
[2026-05-28T23:03:14.059442Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskRunner:CallGenome+SNV_index_vcf] Task initiated on local node
[2026-05-28T23:03:14.060440Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskRunner:CallGenome+Indel_index_vcf] Task initiated on local node
[2026-05-28T23:03:14.090106Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Completed command task: 'CallGenome+SNV_index_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:14.090172Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Completed command task: 'CallGenome+Indel_index_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:14.090331Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2026-05-28T23:03:14.092471Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2026-05-28T23:03:14.123309Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:19.588172Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2026-05-28T23:03:33.764634Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Strelka somatic workflow successfully completed.
[2026-05-28T23:03:33.764634Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] 
[2026-05-28T23:03:33.764634Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] 	workflow version: 2.9.10
[2026-05-28T23:03:33.764716Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] 
[2026-05-28T23:03:33.764724Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-05-28T23:03:33.764731Z] [nf-bb13d2fa860f2962f35958befd8263c4-5093b-2jmpp] [660_1] [WorkflowRunner] Elapsed time for full workflow: 33 sec