[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXUOin7I/chr21_5117003-5117331.bed.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXUOin7I/chr21_5117003-5117331.bed.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXUOin7I/chr21_5117003-5117331.bed.gz.tbi
[2026-06-05T15:20:44.688021Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Initiating pyFlow run
[2026-06-05T15:20:44.730356Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaSomaticWorkflow
[2026-06-05T15:20:44.730391Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-06-05T15:20:44.730398Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-06-05T15:20:44.730403Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXUOin7I'
[2026-06-05T15:20:44.730408Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/strelka/runWorkflow.py -m local -j 8'
[2026-06-05T15:20:44.730414Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] [RunParameters] mode: local
[2026-06-05T15:20:44.730418Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] [RunParameters] nCores: 8
[2026-06-05T15:20:44.730422Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] [RunParameters] memMb: 3096076
[2026-06-05T15:20:44.730426Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/strelka/workspace/pyflow.data
[2026-06-05T15:20:44.730431Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-06-05T15:20:44.730435Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-06-05T15:20:44.730439Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-06-05T15:20:44.730443Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-06-05T15:20:44.730947Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-06-05T15:20:44.731058Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [StrelkaSomaticWorkflow] Initiating Strelka somatic workflow version: 2.9.10
[2026-06-05T15:20:44.736647Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2026-06-05T15:20:44.737241Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2026-06-05T15:20:44.737454Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-06-05T15:20:44.737685Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2026-06-05T15:20:44.737904Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2026-06-05T15:20:44.738993Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-05T15:20:44.739206Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-05T15:20:44.739583Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-05T15:20:44.739721Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2026-06-05T15:20:44.740080Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-05T15:20:44.740559Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-05T15:20:44.740968Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-05T15:20:44.741126Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-05T15:20:44.742840Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2026-06-05T15:20:44.756804Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-05T15:20:44.756929Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-05T15:20:44.757003Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2026-06-05T15:20:44.757092Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-05T15:20:44.757164Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2026-06-05T15:20:44.757234Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-05T15:20:44.757676Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2026-06-05T15:20:44.757798Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2026-06-05T15:20:44.757882Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2026-06-05T15:20:44.757937Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2026-06-05T15:20:44.774358Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:44.774661Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-05T15:20:44.775579Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-05T15:20:44.778212Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0000] Task initiated on local node
[2026-06-05T15:20:44.778755Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-05T15:20:44.779107Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0003] Task initiated on local node
[2026-06-05T15:20:44.779443Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-05T15:20:44.783245Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0001] Task initiated on local node
[2026-06-05T15:20:44.784271Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0002] Task initiated on local node
[2026-06-05T15:20:44.894558Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:44.895080Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-05T15:20:44.901751Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0003] Task initiated on local node
[2026-06-05T15:20:44.971896Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:47.218062Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:47.218483Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Launching command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-05T15:20:47.221842Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskRunner:CallGenome+fixVcfHeader_chromId_020_chr21_0000] Task initiated on local node
[2026-06-05T15:20:47.282955Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Completed command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:47.283271Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-05T15:20:47.285909Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0000] Task initiated on local node
[2026-06-05T15:20:47.347451Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:47.762341Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:47.762748Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-05T15:20:47.765496Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0001] Task initiated on local node
[2026-06-05T15:20:47.796109Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:59.864834Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:59.865752Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-05T15:20:59.868877Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0002] Task initiated on local node
[2026-06-05T15:20:59.930354Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:59.930527Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:59.930658Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Launching command task: 'CallGenome+Indel_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-05T15:20:59.931280Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2026-06-05T15:20:59.933276Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Launching command task: 'CallGenome+SNV_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-05T15:20:59.933552Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskRunner:CallGenome+Indel_concat_vcf] Task initiated on local node
[2026-06-05T15:20:59.936430Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2026-06-05T15:20:59.937355Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskRunner:CallGenome+SNV_concat_vcf] Task initiated on local node
[2026-06-05T15:20:59.968354Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Completed command task: 'CallGenome+SNV_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:59.968419Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Completed command task: 'CallGenome+Indel_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:59.968445Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:59.968631Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Launching command task: 'CallGenome+Indel_index_vcf' from sub-workflow 'CallGenome'
[2026-06-05T15:20:59.970206Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Launching command task: 'CallGenome+SNV_index_vcf' from sub-workflow 'CallGenome'
[2026-06-05T15:20:59.971787Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskRunner:CallGenome+Indel_index_vcf] Task initiated on local node
[2026-06-05T15:20:59.972737Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskRunner:CallGenome+SNV_index_vcf] Task initiated on local node
[2026-06-05T15:21:00.002581Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Completed command task: 'CallGenome+SNV_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-05T15:21:00.002652Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Completed command task: 'CallGenome+Indel_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-05T15:21:00.002827Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2026-06-05T15:21:00.005027Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2026-06-05T15:21:00.034971Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-05T15:21:03.656481Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2026-06-05T15:21:17.849721Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Strelka somatic workflow successfully completed.
[2026-06-05T15:21:17.849721Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] 
[2026-06-05T15:21:17.849721Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] 	workflow version: 2.9.10
[2026-06-05T15:21:17.849836Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] 
[2026-06-05T15:21:17.849845Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-06-05T15:21:17.849854Z] [nf-e10d942bd5087f41384e18c972769b92-ae55b-mh47w] [733_1] [WorkflowRunner] Elapsed time for full workflow: 33 sec