File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/cb4f5b94e096005f6193a6d1fc9087/.command.log
Size
1.1 KB
Task
NFCORE_HARMONIZE:HARMONIZE:HARMONIZE_SV:HARMONIZE_SV_ALTERA_INHOUSE_DNA:MANTA_SV_NORMALIZE (FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1)
Attempt

Content

View in new tab 
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0035/tools__44c19e3d--20260605-213512/annotation/manta/FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1/FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/cb4f5b94e096005f6193a6d1fc9087/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/cb4f5b94e096005f6193a6d1fc9087/.command.sh
==> STAGING COMPLETE (3 inputs)

Parsing Manta VCF: FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann.vcf.gz
  Found 332 SV records
  TSV written to: FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.sv.hmnz.tsv
  BEDPE written to: FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.sv.hmnz.bedpe
  SV type counts: {'DEL': 240, 'DUP': 29, 'INS': 23, 'BND': 40}
  Records with gene1 annotation: 332/332
ls: *.vcf.gz.tbi: No such file or directory