File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/6d9a208decfc2a795ee8ce4906d3f9/.command.log
Size
1.0 KB
Task
NFCORE_HARMONIZE:HARMONIZE:HARMONIZE_SV:HARMONIZE_SV_ALTERA_INHOUSE_DNA:MANTA_SV_NORMALIZE (869_VZQ-T1-TDNA-1_A23WGJTLT4_3_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/6d9a208decfc2a795ee8ce4906d3f9/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0034/tools__44c19e3d--20260605-212233/annotation/manta/869_VZQ-T1-TDNA-1_A23WGJTLT4_3_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1/869_VZQ-T1-TDNA-1_A23WGJTLT4_3_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/6d9a208decfc2a795ee8ce4906d3f9/.command.run
==> STAGING COMPLETE (3 inputs)

Parsing Manta VCF: 869_VZQ-T1-TDNA-1_A23WGJTLT4_3_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann.vcf.gz
  Found 83 SV records
  TSV written to: 869_VZQ-T1-TDNA-1_A23WGJTLT4_3_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.sv.hmnz.tsv
  BEDPE written to: 869_VZQ-T1-TDNA-1_A23WGJTLT4_3_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.sv.hmnz.bedpe
  SV type counts: {'DEL': 57, 'INS': 6, 'BND': 12, 'DUP': 8}
  Records with gene1 annotation: 83/83
ls: *.vcf.gz.tbi: No such file or directory