File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/fd868dd965ae7551fc982a83c80115/.command.log
Size
1.1 KB
Task
NFCORE_HARMONIZE:HARMONIZE:HARMONIZE_SV:HARMONIZE_SV_ALTERA_INHOUSE_DNA:MANTA_SV_NORMALIZE (PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1)
Attempt

Content

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  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0035/tools__44c19e3d--20260605-213512/annotation/manta/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/fd868dd965ae7551fc982a83c80115/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/fd868dd965ae7551fc982a83c80115/.command.sh
==> STAGING COMPLETE (3 inputs)

Parsing Manta VCF: PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann.vcf.gz
  Found 119 SV records
  TSV written to: PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.sv.hmnz.tsv
  BEDPE written to: PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.sv.hmnz.bedpe
  SV type counts: {'DEL': 22, 'BND': 80, 'DUP': 14, 'INS': 3}
  Records with gene1 annotation: 119/119
ls: *.vcf.gz.tbi: No such file or directory