File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/1051e3cb28fa7c4dc1411d32da2b08/.command.log
Size
1.6 KB
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:VCF_SOMATIC_SNV_INDEL:HARD_FILTER_VCF (custom_Sig_18_tumor_normal)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/6782f4f1608fddd7e6b2828f65adfc/custom_Sig_18_tumor_normal.snv_indel.annotated.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/1051e3cb28fa7c4dc1411d32da2b08/.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/e3/6782f4f1608fddd7e6b2828f65adfc/custom_Sig_18_tumor_normal.snv_indel.annotated.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
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/1051e3cb28fa7c4dc1411d32da2b08/.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: 252 variants processed, 8 PASS
  low_tumor_dp: 4
  low_normal_dp: 4
  low_tumor_alt: 9
  high_normal_vaf: 176
  panel_of_normals: 68
  panel_of_tumors: 0