File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/e5e7cf23b0db7b5800f1f22beb674d/.command.log
Size
1.1 KB
Task
NFCORE_HARMONIZE:HARMONIZE:HARMONIZE_SV:HARMONIZE_SV_ALTERA_INHOUSE_DNA:MANTA_SV_NORMALIZE (1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_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/1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1/1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/e5e7cf23b0db7b5800f1f22beb674d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/e5e7cf23b0db7b5800f1f22beb674d/.command.sh
==> STAGING COMPLETE (3 inputs)

Parsing Manta VCF: 1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann.vcf.gz
  Found 125 SV records
  TSV written to: 1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.sv.hmnz.tsv
  BEDPE written to: 1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.sv.hmnz.bedpe
  SV type counts: {'BND': 88, 'DEL': 18, 'DUP': 18, 'INS': 1}
  Records with gene1 annotation: 125/125
ls: *.vcf.gz.tbi: No such file or directory