[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXwTN1tv/chr21_34799195-34799564.bed.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXwTN1tv/chr21_34799195-34799564.bed.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXwTN1tv/chr21_34799195-34799564.bed.gz.tbi
[2026-05-28T20:33:17.592723Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Initiating pyFlow run
[2026-05-28T20:33:17.595889Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaSomaticWorkflow
[2026-05-28T20:33:17.595916Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-05-28T20:33:17.595925Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-05-28T20:33:17.595936Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXwTN1tv'
[2026-05-28T20:33:17.595944Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/strelka/runWorkflow.py -m local -j 8'
[2026-05-28T20:33:17.595954Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] [RunParameters] mode: local
[2026-05-28T20:33:17.595966Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] [RunParameters] nCores: 8
[2026-05-28T20:33:17.595972Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] [RunParameters] memMb: 1523801
[2026-05-28T20:33:17.595982Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/strelka/workspace/pyflow.data
[2026-05-28T20:33:17.595988Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-05-28T20:33:17.595996Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-05-28T20:33:17.596003Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-05-28T20:33:17.596011Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-05-28T20:33:17.596395Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-05-28T20:33:17.596496Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [StrelkaSomaticWorkflow] Initiating Strelka somatic workflow version: 2.9.10
[2026-05-28T20:33:17.603438Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2026-05-28T20:33:17.604038Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-05-28T20:33:17.604207Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2026-05-28T20:33:17.604338Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2026-05-28T20:33:17.604528Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2026-05-28T20:33:17.605644Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-05-28T20:33:17.605817Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-05-28T20:33:17.606155Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-05-28T20:33:17.606407Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-05-28T20:33:17.606457Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2026-05-28T20:33:17.606750Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-05-28T20:33:17.607336Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-05-28T20:33:17.607868Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-05-28T20:33:17.635963Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-05-28T20:33:17.636419Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2026-05-28T20:33:17.636510Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-05-28T20:33:17.636688Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2026-05-28T20:33:17.636870Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2026-05-28T20:33:17.637078Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2026-05-28T20:33:17.637224Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2026-05-28T20:33:17.637356Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2026-05-28T20:33:17.637538Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2026-05-28T20:33:17.637683Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2026-05-28T20:33:17.637812Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2026-05-28T20:33:17.676973Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2026-05-28T20:33:17.677257Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-05-28T20:33:17.677722Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-05-28T20:33:17.678272Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-05-28T20:33:17.679220Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-05-28T20:33:17.685058Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0003] Task initiated on local node
[2026-05-28T20:33:17.686863Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0000] Task initiated on local node
[2026-05-28T20:33:17.689112Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0002] Task initiated on local node
[2026-05-28T20:33:17.689671Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0001] Task initiated on local node
[2026-05-28T20:33:17.794825Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-05-28T20:33:17.794900Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-05-28T20:33:17.795247Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-05-28T20:33:17.795528Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Launching command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-05-28T20:33:17.799200Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0001] Task initiated on local node
[2026-05-28T20:33:17.835890Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskRunner:CallGenome+fixVcfHeader_chromId_020_chr21_0000] Task initiated on local node
[2026-05-28T20:33:17.859936Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-05-28T20:33:17.863346Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Completed command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-05-28T20:33:17.863626Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-05-28T20:33:17.866299Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0000] Task initiated on local node
[2026-05-28T20:33:17.927513Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-05-28T20:33:24.093628Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-05-28T20:33:24.094065Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-05-28T20:33:24.097215Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0002] Task initiated on local node
[2026-05-28T20:33:24.158182Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-05-28T20:36:47.595470Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-05-28T20:36:47.596336Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-05-28T20:36:47.599009Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0003] Task initiated on local node
[2026-05-28T20:36:47.660370Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-05-28T20:36:47.660635Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2026-05-28T20:36:47.660863Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2026-05-28T20:36:47.661277Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Launching command task: 'CallGenome+Indel_concat_vcf' from sub-workflow 'CallGenome'
[2026-05-28T20:36:47.661820Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Launching command task: 'CallGenome+SNV_concat_vcf' from sub-workflow 'CallGenome'
[2026-05-28T20:36:47.665231Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2026-05-28T20:36:47.667893Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskRunner:CallGenome+SNV_concat_vcf] Task initiated on local node
[2026-05-28T20:36:47.695211Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskRunner:CallGenome+Indel_concat_vcf] Task initiated on local node
[2026-05-28T20:36:47.727581Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2026-05-28T20:36:47.727663Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Completed command task: 'CallGenome+Indel_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T20:36:47.727713Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Completed command task: 'CallGenome+SNV_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T20:36:47.728127Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Launching command task: 'CallGenome+SNV_index_vcf' from sub-workflow 'CallGenome'
[2026-05-28T20:36:47.728548Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Launching command task: 'CallGenome+Indel_index_vcf' from sub-workflow 'CallGenome'
[2026-05-28T20:36:47.731679Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskRunner:CallGenome+Indel_index_vcf] Task initiated on local node
[2026-05-28T20:36:47.763123Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskRunner:CallGenome+SNV_index_vcf] Task initiated on local node
[2026-05-28T20:36:47.793591Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Completed command task: 'CallGenome+SNV_index_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T20:36:47.793685Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Completed command task: 'CallGenome+Indel_index_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T20:36:47.794035Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2026-05-28T20:36:47.796725Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2026-05-28T20:36:47.858087Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2026-05-28T20:36:50.876761Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2026-05-28T20:37:05.866767Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Strelka somatic workflow successfully completed.
[2026-05-28T20:37:05.866767Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] 
[2026-05-28T20:37:05.866767Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] 	workflow version: 2.9.10
[2026-05-28T20:37:05.866878Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] 
[2026-05-28T20:37:05.866892Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-05-28T20:37:05.866905Z] [nf-ff6d36ec7098a14d173f04b91b881a1f-df62d-cqpmf] [818_1] [WorkflowRunner] Elapsed time for full workflow: 228 sec