[2026-06-05T15:20:43.551789Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Initiating pyFlow run
[2026-06-05T15:20:43.552798Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaSomaticWorkflow
[2026-06-05T15:20:43.552810Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-06-05T15:20:43.552814Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-06-05T15:20:43.552819Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXl5pntr'
[2026-06-05T15:20:43.552822Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/strelka/runWorkflow.py -m local -j 8'
[2026-06-05T15:20:43.552827Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] [RunParameters] mode: local
[2026-06-05T15:20:43.552830Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] [RunParameters] nCores: 8
[2026-06-05T15:20:43.552834Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] [RunParameters] memMb: 3047507
[2026-06-05T15:20:43.552838Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/strelka/workspace/pyflow.data
[2026-06-05T15:20:43.552841Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-06-05T15:20:43.552845Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-06-05T15:20:43.552848Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-06-05T15:20:43.552852Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-06-05T15:20:43.553608Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-06-05T15:20:43.553734Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [StrelkaSomaticWorkflow] Initiating Strelka somatic workflow version: 2.9.10
[2026-06-05T15:20:43.559638Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2026-06-05T15:20:43.560449Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-06-05T15:20:43.560585Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2026-06-05T15:20:43.561045Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2026-06-05T15:20:43.561294Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2026-06-05T15:20:43.562220Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-05T15:20:43.562315Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-05T15:20:43.562387Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-05T15:20:43.562715Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-05T15:20:43.563037Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-05T15:20:43.563184Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2026-06-05T15:20:43.563456Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-05T15:20:43.563537Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-05T15:20:43.579059Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-05T15:20:43.580362Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-05T15:20:43.580559Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2026-06-05T15:20:43.580929Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-05T15:20:43.581387Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2026-06-05T15:20:43.581547Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2026-06-05T15:20:43.581746Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-05T15:20:43.582079Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2026-06-05T15:20:43.582298Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2026-06-05T15:20:43.582368Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2026-06-05T15:20:43.582420Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2026-06-05T15:20:43.615059Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:43.615377Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-05T15:20:43.616167Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-05T15:20:43.617506Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-05T15:20:43.618371Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0000] Task initiated on local node
[2026-06-05T15:20:43.619820Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-05T15:20:43.620710Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0001] Task initiated on local node
[2026-06-05T15:20:43.623591Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0003] Task initiated on local node
[2026-06-05T15:20:43.624209Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0002] Task initiated on local node
[2026-06-05T15:20:43.684539Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:43.684607Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:43.684863Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Launching command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-05T15:20:43.685306Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-05T15:20:43.687707Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskRunner:CallGenome+fixVcfHeader_chromId_020_chr21_0000] Task initiated on local node
[2026-06-05T15:20:43.688812Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0001] Task initiated on local node
[2026-06-05T15:20:43.689603Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:43.689832Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-05T15:20:43.692075Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0002] Task initiated on local node
[2026-06-05T15:20:43.721729Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:43.721795Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:43.737467Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Completed command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:43.737716Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-05T15:20:43.740356Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0000] Task initiated on local node
[2026-06-05T15:20:43.801846Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:57.524550Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:57.525360Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-05T15:20:57.528054Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0003] Task initiated on local node
[2026-06-05T15:20:57.589342Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:57.589549Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:57.589699Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2026-06-05T15:20:57.590073Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Launching command task: 'CallGenome+Indel_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-05T15:20:57.590717Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Launching command task: 'CallGenome+SNV_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-05T15:20:57.593795Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskRunner:CallGenome+Indel_concat_vcf] Task initiated on local node
[2026-06-05T15:20:57.595654Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2026-06-05T15:20:57.596682Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskRunner:CallGenome+SNV_concat_vcf] Task initiated on local node
[2026-06-05T15:20:57.624138Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Completed command task: 'CallGenome+Indel_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:57.624214Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:57.624243Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Completed command task: 'CallGenome+SNV_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:57.624475Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Launching command task: 'CallGenome+Indel_index_vcf' from sub-workflow 'CallGenome'
[2026-06-05T15:20:57.624834Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Launching command task: 'CallGenome+SNV_index_vcf' from sub-workflow 'CallGenome'
[2026-06-05T15:20:57.627490Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskRunner:CallGenome+Indel_index_vcf] Task initiated on local node
[2026-06-05T15:20:57.628288Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskRunner:CallGenome+SNV_index_vcf] Task initiated on local node
[2026-06-05T15:20:57.656791Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Completed command task: 'CallGenome+Indel_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:57.656865Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Completed command task: 'CallGenome+SNV_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-05T15:20:57.657064Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2026-06-05T15:20:57.659167Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2026-06-05T15:20:57.688827Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-05T15:21:02.463640Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2026-06-05T15:21:16.672062Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Strelka somatic workflow successfully completed.
[2026-06-05T15:21:16.672062Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner]
[2026-06-05T15:21:16.672062Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] workflow version: 2.9.10
[2026-06-05T15:21:16.672146Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner]
[2026-06-05T15:21:16.672155Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-06-05T15:21:16.672162Z] [nf-dff6ec1cbf1c9b15dded8103141d41d6-adce1-tlrmz] [719_1] [WorkflowRunner] Elapsed time for full workflow: 33 sec