[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXSn8P6D/chr21_34799195-34799564.bed.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXSn8P6D/chr21_34799195-34799564.bed.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXSn8P6D/chr21_34799195-34799564.bed.gz.tbi
[2026-06-05T01:59:21.476161Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Initiating pyFlow run
[2026-06-05T01:59:21.476937Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaSomaticWorkflow
[2026-06-05T01:59:21.476947Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-06-05T01:59:21.476952Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-06-05T01:59:21.476956Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXSn8P6D'
[2026-06-05T01:59:21.476960Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/strelka/runWorkflow.py -m local -j 8'
[2026-06-05T01:59:21.476964Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] [RunParameters] mode: local
[2026-06-05T01:59:21.476968Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] [RunParameters] nCores: 8
[2026-06-05T01:59:21.476971Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] [RunParameters] memMb: 1547923
[2026-06-05T01:59:21.476975Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/strelka/workspace/pyflow.data
[2026-06-05T01:59:21.476978Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-06-05T01:59:21.476982Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-06-05T01:59:21.476985Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-06-05T01:59:21.476989Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-06-05T01:59:21.477620Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-06-05T01:59:21.477735Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [StrelkaSomaticWorkflow] Initiating Strelka somatic workflow version: 2.9.10
[2026-06-05T01:59:21.483376Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2026-06-05T01:59:21.483999Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2026-06-05T01:59:21.484213Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2026-06-05T01:59:21.484717Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2026-06-05T01:59:21.485173Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-06-05T01:59:21.485561Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2026-06-05T01:59:21.487263Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-05T01:59:21.488801Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-05T01:59:21.488984Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-05T01:59:21.489224Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-05T01:59:21.489414Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2026-06-05T01:59:21.489723Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-05T01:59:21.489968Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-05T01:59:21.490039Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-05T01:59:21.501152Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-05T01:59:21.501253Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-05T01:59:21.501323Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2026-06-05T01:59:21.501407Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-05T01:59:21.501477Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2026-06-05T01:59:21.501546Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-05T01:59:21.501610Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2026-06-05T01:59:21.501690Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2026-06-05T01:59:21.501757Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2026-06-05T01:59:21.501801Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2026-06-05T01:59:21.514945Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-05T01:59:21.515241Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-05T01:59:21.515996Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-05T01:59:21.516617Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-05T01:59:21.517546Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-05T01:59:21.520192Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0001] Task initiated on local node
[2026-06-05T01:59:21.521122Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0003] Task initiated on local node
[2026-06-05T01:59:21.523520Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0000] Task initiated on local node
[2026-06-05T01:59:21.524250Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0002] Task initiated on local node
[2026-06-05T01:59:21.583731Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-05T01:59:21.584093Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-05T01:59:21.586345Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0001] Task initiated on local node
[2026-06-05T01:59:21.588106Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-05T01:59:21.588410Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Launching command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-05T01:59:21.590463Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskRunner:CallGenome+fixVcfHeader_chromId_020_chr21_0000] Task initiated on local node
[2026-06-05T01:59:21.621145Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-05T01:59:21.636947Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Completed command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-05T01:59:21.637240Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-05T01:59:21.639800Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0000] Task initiated on local node
[2026-06-05T01:59:21.701537Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-05T01:59:22.918545Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-05T01:59:22.918938Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-05T01:59:22.921352Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0002] Task initiated on local node
[2026-06-05T01:59:22.951057Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-05T01:59:51.473368Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-05T01:59:51.474297Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-05T01:59:51.476609Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0003] Task initiated on local node
[2026-06-05T01:59:51.506321Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-05T01:59:51.506490Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2026-06-05T01:59:51.506620Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Launching command task: 'CallGenome+Indel_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-05T01:59:51.507235Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2026-06-05T01:59:51.508883Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Launching command task: 'CallGenome+SNV_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-05T01:59:51.509490Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskRunner:CallGenome+Indel_concat_vcf] Task initiated on local node
[2026-06-05T01:59:51.511764Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2026-06-05T01:59:51.512401Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskRunner:CallGenome+SNV_concat_vcf] Task initiated on local node
[2026-06-05T01:59:51.542051Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Completed command task: 'CallGenome+SNV_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-05T01:59:51.542118Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Completed command task: 'CallGenome+Indel_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-05T01:59:51.542142Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2026-06-05T01:59:51.542331Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Launching command task: 'CallGenome+Indel_index_vcf' from sub-workflow 'CallGenome'
[2026-06-05T01:59:51.542941Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Launching command task: 'CallGenome+SNV_index_vcf' from sub-workflow 'CallGenome'
[2026-06-05T01:59:51.545089Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskRunner:CallGenome+Indel_index_vcf] Task initiated on local node
[2026-06-05T01:59:51.545971Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskRunner:CallGenome+SNV_index_vcf] Task initiated on local node
[2026-06-05T01:59:51.575731Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Completed command task: 'CallGenome+SNV_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-05T01:59:51.575805Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Completed command task: 'CallGenome+Indel_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-05T01:59:51.575984Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2026-06-05T01:59:51.578040Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2026-06-05T01:59:51.608742Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-05T01:59:54.628371Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2026-06-05T02:00:09.596137Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Strelka somatic workflow successfully completed.
[2026-06-05T02:00:09.596137Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner]
[2026-06-05T02:00:09.596137Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] workflow version: 2.9.10
[2026-06-05T02:00:09.596227Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner]
[2026-06-05T02:00:09.596237Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-06-05T02:00:09.596244Z] [nf-c251ba3de565da7040cb4a7e7621bb85-554f8-46z2h] [698_1] [WorkflowRunner] Elapsed time for full workflow: 48 sec