File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/66891b03fc90e83151fc7ab3e6bcc5/.command.log
Size
1.6 KB
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:VCF_SOMATIC_SNV_INDEL:HARD_FILTER_VCF (HCC1395_tumor_vs_HCC1395_BL)
Attempt

Content

View in new tab 
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/66891b03fc90e83151fc7ab3e6bcc5/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/POT/aih_tumor_1577_pot_1pct_artifacts_only.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/PON/pon_tnseq_42_curated_v4.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/POT/aih_tumor_1577_pot_1pct_artifacts_only.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/ad93cfd1a7dfe9467de3be3fbd07d3/HCC1395_tumor_vs_HCC1395_BL.snv_indel.annotated.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/PON/pon_tnseq_42_curated_v4.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/ad93cfd1a7dfe9467de3be3fbd07d3/HCC1395_tumor_vs_HCC1395_BL.snv_indel.annotated.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/66891b03fc90e83151fc7ab3e6bcc5/.command.run
==> STAGING COMPLETE (8 inputs)

Loading PON positions from pon_tnseq_42_curated_v4.vcf.gz
  Loaded 550,680 PON positions
Loading POT positions from aih_tumor_1577_pot_1pct_artifacts_only.vcf.gz
  Loaded 545 POT positions
Hard filter summary: 187 variants processed, 6 PASS
  low_tumor_dp: 2
  low_normal_dp: 2
  low_tumor_alt: 21
  high_normal_vaf: 154
  panel_of_normals: 38
  panel_of_tumors: 1