Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/regression_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed.gz.tbi
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/253e9038d239bba3c7ead946c79ea2/.command.sh
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_tissue/Sig_18_tissue.recalibrated.bam
Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_tissue/Sig_18_tissue.recalibrated.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/253e9038d239bba3c7ead946c79ea2/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_Blood/Sig_18_Blood.recalibrated.bam.bai
Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_Blood/Sig_18_Blood.recalibrated.bam
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/regression_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed.gz
==> STAGING COMPLETE (10 inputs)
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXMkn8R0/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXMkn8R0/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXMkn8R0/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed.gz.tbi
Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:
/var/tmp/manta/runWorkflow.py
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXMkn8R0/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXMkn8R0/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed.gz.tbi
[2026-06-08T20:42:56.250422Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Initiating pyFlow run
[2026-06-08T20:42:56.251638Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] pyFlowClientWorkflowClass: MantaWorkflow
[2026-06-08T20:42:56.251650Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-06-08T20:42:56.251654Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-06-08T20:42:56.251658Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXMkn8R0'
[2026-06-08T20:42:56.251663Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/manta/runWorkflow.py -m local -j 14'
[2026-06-08T20:42:56.251670Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] [RunParameters] mode: local
[2026-06-08T20:42:56.251674Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] [RunParameters] nCores: 14
[2026-06-08T20:42:56.251678Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] [RunParameters] memMb: 3096076
[2026-06-08T20:42:56.251682Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/manta/workspace/pyflow.data
[2026-06-08T20:42:56.251687Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-06-08T20:42:56.251691Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-06-08T20:42:56.251695Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-06-08T20:42:56.251699Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-06-08T20:42:56.252443Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-06-08T20:42:56.252524Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [MantaWorkflow] Initiating Manta workflow version: 1.6.0
[2026-06-08T20:42:56.252839Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'getAlignmentStats_makeTmpDir' to master workflow
[2026-06-08T20:42:56.253487Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'getAlignmentStats_generateStats_000' to master workflow
[2026-06-08T20:42:56.253796Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'getAlignmentStats_generateStats_001' to master workflow
[2026-06-08T20:42:56.253894Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'getAlignmentStats_makeTmpDir' from master workflow
[2026-06-08T20:42:56.254168Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'getAlignmentStats_mergeStats' to master workflow
[2026-06-08T20:42:56.254774Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'getAlignmentStats_removeTmpDir' to master workflow
[2026-06-08T20:42:56.255229Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'summarizeStats' to master workflow
[2026-06-08T20:42:56.258041Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'makeGraphTmpDir' to master workflow
[2026-06-08T20:42:56.259477Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:getAlignmentStats_makeTmpDir] Task initiated on local node
[2026-06-08T20:42:56.323204Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'getAlignmentStats_makeTmpDir' launched from master workflow
[2026-06-08T20:42:56.323834Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'getAlignmentStats_generateStats_000' from master workflow
[2026-06-08T20:42:56.324904Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'getAlignmentStats_generateStats_001' from master workflow
[2026-06-08T20:42:56.330578Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:getAlignmentStats_generateStats_001] Task initiated on local node
[2026-06-08T20:42:56.588378Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'makeLocusGraph_chromId_020_chr21-5117103-5117231_0000_to_chromId_020_chr21-39269899-39270033_0000' to master workflow
[2026-06-08T20:42:56.928185Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'makeLocusGraph_chromId_020_chr21-39270283-39270433_0000_to_chromId_020_chr21-46664295-46664374_0000' to master workflow
[2026-06-08T20:42:56.928527Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding sub-workflow task 'mergeLocusGraphInputList' to master workflow
[2026-06-08T20:42:56.928628Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'mergeLocusGraph' to master workflow
[2026-06-08T20:42:56.928704Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'checkLocusGraph' to master workflow
[2026-06-08T20:42:56.928777Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'removeTmpDir' to master workflow
[2026-06-08T20:42:56.928866Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'locusGraphStats' to master workflow
[2026-06-08T20:42:56.929134Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'makeHyGenDir' to master workflow
[2026-06-08T20:42:56.929273Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'generateCandidateSV_0000' to master workflow
[2026-06-08T20:42:56.929378Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'fixVcfHeader_sortCandidateSV' to master workflow
[2026-06-08T20:42:56.929496Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding sub-workflow task 'sortCandidateSVInputList' to master workflow
[2026-06-08T20:42:56.929569Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'sort_sortCandidateSV' to master workflow
[2026-06-08T20:42:56.929644Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'tabix_sortCandidateSV' to master workflow
[2026-06-08T20:42:56.929719Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'fixVcfHeader_sortDiploidSV' to master workflow
[2026-06-08T20:42:56.929823Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding sub-workflow task 'sortDiploidSVInputList' to master workflow
[2026-06-08T20:42:56.929902Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'sort_sortDiploidSV' to master workflow
[2026-06-08T20:42:56.929981Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'tabix_sortDiploidSV' to master workflow
[2026-06-08T20:42:56.930054Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'fixVcfHeader_sortSomaticSV' to master workflow
[2026-06-08T20:42:56.930155Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding sub-workflow task 'sortSomaticSVInputList' to master workflow
[2026-06-08T20:42:56.930225Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'sort_sortSomaticSV' to master workflow
[2026-06-08T20:42:56.930293Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'tabix_sortSomaticSV' to master workflow
[2026-06-08T20:42:56.930377Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'extractSmallIndels' to master workflow
[2026-06-08T20:42:56.930446Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'extractSmallIndels_tabix' to master workflow
[2026-06-08T20:42:56.930552Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding sub-workflow task 'sortEdgeRuntimeLogsInputList' to master workflow
[2026-06-08T20:42:56.930629Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Adding command task 'sortEdgeRuntimeLogs' to master workflow
[2026-06-08T20:42:56.930675Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-06-08T20:43:11.051167Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
[2026-06-08T20:43:11.082671Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'getAlignmentStats_generateStats_000' launched from master workflow
[2026-06-08T20:43:11.082748Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'getAlignmentStats_generateStats_001' launched from master workflow
[2026-06-08T20:43:11.083849Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'getAlignmentStats_mergeStats' from master workflow
[2026-06-08T20:43:11.086566Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:getAlignmentStats_mergeStats] Task initiated on local node
[2026-06-08T20:43:11.147946Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'getAlignmentStats_mergeStats' launched from master workflow
[2026-06-08T20:43:11.148336Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'getAlignmentStats_removeTmpDir' from master workflow
[2026-06-08T20:43:11.148990Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'makeGraphTmpDir' from master workflow
[2026-06-08T20:43:11.150975Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'summarizeStats' from master workflow
[2026-06-08T20:43:11.151316Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:getAlignmentStats_removeTmpDir] Task initiated on local node
[2026-06-08T20:43:11.154163Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:makeGraphTmpDir] Task initiated on local node
[2026-06-08T20:43:11.154997Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:summarizeStats] Task initiated on local node
[2026-06-08T20:43:11.184434Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'getAlignmentStats_removeTmpDir' launched from master workflow
[2026-06-08T20:43:11.184500Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'summarizeStats' launched from master workflow
[2026-06-08T20:43:11.184524Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'makeGraphTmpDir' launched from master workflow
[2026-06-08T20:43:11.184851Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'makeLocusGraph_chromId_020_chr21-39270283-39270433_0000_to_chromId_020_chr21-46664295-46664374_0000' from master workflow
[2026-06-08T20:43:11.185395Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'makeLocusGraph_chromId_020_chr21-5117103-5117231_0000_to_chromId_020_chr21-39269899-39270033_0000' from master workflow
[2026-06-08T20:43:11.203846Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:makeLocusGraph_chromId_020_chr21-39270283-39270433_0000_to_chromId_020_chr21-46664295-46664374_0000] Task initiated on local node
[2026-06-08T20:43:11.204802Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:makeLocusGraph_chromId_020_chr21-5117103-5117231_0000_to_chromId_020_chr21-39269899-39270033_0000] Task initiated on local node
[2026-06-08T20:43:28.455383Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'makeLocusGraph_chromId_020_chr21-5117103-5117231_0000_to_chromId_020_chr21-39269899-39270033_0000' launched from master workflow
[2026-06-08T20:43:40.274443Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'makeLocusGraph_chromId_020_chr21-39270283-39270433_0000_to_chromId_020_chr21-46664295-46664374_0000' launched from master workflow
[2026-06-08T20:43:40.275391Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching sub-workflow task: 'mergeLocusGraphInputList' from master workflow
[2026-06-08T20:43:40.275631Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:mergeLocusGraphInputList] Starting task specification for sub-workflow
[2026-06-08T20:43:40.275804Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:mergeLocusGraphInputList] Finished task specification for sub-workflow
[2026-06-08T20:43:40.276238Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed sub-workflow task: 'mergeLocusGraphInputList' launched from master workflow
[2026-06-08T20:43:40.276618Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'mergeLocusGraph' from master workflow
[2026-06-08T20:43:40.279652Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:mergeLocusGraph] Task initiated on local node
[2026-06-08T20:43:40.340832Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'mergeLocusGraph' launched from master workflow
[2026-06-08T20:43:40.341195Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'locusGraphStats' from master workflow
[2026-06-08T20:43:40.342982Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'checkLocusGraph' from master workflow
[2026-06-08T20:43:40.343516Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:locusGraphStats] Task initiated on local node
[2026-06-08T20:43:40.343952Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'removeTmpDir' from master workflow
[2026-06-08T20:43:40.346606Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:checkLocusGraph] Task initiated on local node
[2026-06-08T20:43:40.347794Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:removeTmpDir] Task initiated on local node
[2026-06-08T20:43:40.377314Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'locusGraphStats' launched from master workflow
[2026-06-08T20:43:40.377380Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'checkLocusGraph' launched from master workflow
[2026-06-08T20:43:40.377402Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'removeTmpDir' launched from master workflow
[2026-06-08T20:43:40.377699Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'makeHyGenDir' from master workflow
[2026-06-08T20:43:40.379974Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:makeHyGenDir] Task initiated on local node
[2026-06-08T20:43:40.409779Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'makeHyGenDir' launched from master workflow
[2026-06-08T20:43:40.410115Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'generateCandidateSV_0000' from master workflow
[2026-06-08T20:43:40.412506Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:generateCandidateSV_0000] Task initiated on local node
[2026-06-08T20:43:46.276340Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'generateCandidateSV_0000' launched from master workflow
[2026-06-08T20:43:46.276673Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching sub-workflow task: 'sortEdgeRuntimeLogsInputList' from master workflow
[2026-06-08T20:43:46.276891Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:sortEdgeRuntimeLogsInputList] Starting task specification for sub-workflow
[2026-06-08T20:43:46.277289Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'fixVcfHeader_sortSomaticSV' from master workflow
[2026-06-08T20:43:46.277544Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:sortEdgeRuntimeLogsInputList] Finished task specification for sub-workflow
[2026-06-08T20:43:46.278089Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'fixVcfHeader_sortDiploidSV' from master workflow
[2026-06-08T20:43:46.278742Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'fixVcfHeader_sortCandidateSV' from master workflow
[2026-06-08T20:43:46.281655Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed sub-workflow task: 'sortEdgeRuntimeLogsInputList' launched from master workflow
[2026-06-08T20:43:46.282391Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:fixVcfHeader_sortSomaticSV] Task initiated on local node
[2026-06-08T20:43:46.284234Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:fixVcfHeader_sortDiploidSV] Task initiated on local node
[2026-06-08T20:43:46.284333Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'sortEdgeRuntimeLogs' from master workflow
[2026-06-08T20:43:46.284571Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:fixVcfHeader_sortCandidateSV] Task initiated on local node
[2026-06-08T20:43:46.287283Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:sortEdgeRuntimeLogs] Task initiated on local node
[2026-06-08T20:43:46.348675Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'fixVcfHeader_sortSomaticSV' launched from master workflow
[2026-06-08T20:43:46.348734Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'fixVcfHeader_sortCandidateSV' launched from master workflow
[2026-06-08T20:43:46.348756Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'sortEdgeRuntimeLogs' launched from master workflow
[2026-06-08T20:43:46.348775Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'fixVcfHeader_sortDiploidSV' launched from master workflow
[2026-06-08T20:43:46.348985Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching sub-workflow task: 'sortCandidateSVInputList' from master workflow
[2026-06-08T20:43:46.349164Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:sortCandidateSVInputList] Starting task specification for sub-workflow
[2026-06-08T20:43:46.349449Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching sub-workflow task: 'sortDiploidSVInputList' from master workflow
[2026-06-08T20:43:46.349768Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:sortDiploidSVInputList] Starting task specification for sub-workflow
[2026-06-08T20:43:46.350017Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching sub-workflow task: 'sortSomaticSVInputList' from master workflow
[2026-06-08T20:43:46.350538Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:sortCandidateSVInputList] Finished task specification for sub-workflow
[2026-06-08T20:43:46.350744Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:sortDiploidSVInputList] Finished task specification for sub-workflow
[2026-06-08T20:43:46.350927Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:sortSomaticSVInputList] Starting task specification for sub-workflow
[2026-06-08T20:43:46.351181Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed sub-workflow task: 'sortCandidateSVInputList' launched from master workflow
[2026-06-08T20:43:46.351296Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed sub-workflow task: 'sortDiploidSVInputList' launched from master workflow
[2026-06-08T20:43:46.351536Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'sort_sortCandidateSV' from master workflow
[2026-06-08T20:43:46.353181Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:sortSomaticSVInputList] Finished task specification for sub-workflow
[2026-06-08T20:43:46.353525Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'sort_sortDiploidSV' from master workflow
[2026-06-08T20:43:46.353856Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:sort_sortCandidateSV] Task initiated on local node
[2026-06-08T20:43:46.354122Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed sub-workflow task: 'sortSomaticSVInputList' launched from master workflow
[2026-06-08T20:43:46.354515Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'sort_sortSomaticSV' from master workflow
[2026-06-08T20:43:46.357257Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:sort_sortDiploidSV] Task initiated on local node
[2026-06-08T20:43:46.358341Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:sort_sortSomaticSV] Task initiated on local node
[2026-06-08T20:43:46.419699Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'sort_sortCandidateSV' launched from master workflow
[2026-06-08T20:43:46.419758Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'sort_sortDiploidSV' launched from master workflow
[2026-06-08T20:43:46.419779Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'sort_sortSomaticSV' launched from master workflow
[2026-06-08T20:43:46.419987Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'tabix_sortCandidateSV' from master workflow
[2026-06-08T20:43:46.420598Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'tabix_sortDiploidSV' from master workflow
[2026-06-08T20:43:46.423482Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:tabix_sortCandidateSV] Task initiated on local node
[2026-06-08T20:43:46.423660Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'extractSmallIndels' from master workflow
[2026-06-08T20:43:46.425403Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'tabix_sortSomaticSV' from master workflow
[2026-06-08T20:43:46.425769Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:tabix_sortDiploidSV] Task initiated on local node
[2026-06-08T20:43:46.426408Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:extractSmallIndels] Task initiated on local node
[2026-06-08T20:43:46.428731Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:tabix_sortSomaticSV] Task initiated on local node
[2026-06-08T20:43:46.457873Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'tabix_sortSomaticSV' launched from master workflow
[2026-06-08T20:43:46.457939Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'tabix_sortCandidateSV' launched from master workflow
[2026-06-08T20:43:46.457964Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'tabix_sortDiploidSV' launched from master workflow
[2026-06-08T20:43:46.473594Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'extractSmallIndels' launched from master workflow
[2026-06-08T20:43:46.473801Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Launching command task: 'extractSmallIndels_tabix' from master workflow
[2026-06-08T20:43:46.475974Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskRunner:extractSmallIndels_tabix] Task initiated on local node
[2026-06-08T20:43:46.506028Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [TaskManager] Completed command task: 'extractSmallIndels_tabix' launched from master workflow
[2026-06-08T20:44:00.073651Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Manta workflow successfully completed.
[2026-06-08T20:44:00.073651Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner]
[2026-06-08T20:44:00.073651Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] workflow version: 1.6.0
[2026-06-08T20:44:00.073750Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner]
[2026-06-08T20:44:00.073761Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-06-08T20:44:00.073765Z] [nf-ad253e9038d239bba3c7ead946c79ea2-e46e7-q697r] [614_1] [WorkflowRunner] Elapsed time for full workflow: 63 sec