File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/3d096354599cba0ed99d4cf6940c70/.command.log
Size
1.6 KB
Task
DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:VCF_SOMATIC_SNV_INDEL:HARD_FILTER_VCF (positive_somatic_control_2)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/3d096354599cba0ed99d4cf6940c70/.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-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/e6/3d096354599cba0ed99d4cf6940c70/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/5665cf2e51d8c826be7b0348e35fd0/positive_somatic_control_2.snv_indel.annotated.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/5665cf2e51d8c826be7b0348e35fd0/positive_somatic_control_2.snv_indel.annotated.vcf.gz
==> 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: 184 variants processed, 0 PASS
  low_tumor_dp: 38
  low_normal_dp: 184
  low_tumor_alt: 37
  high_normal_vaf: 104
  panel_of_normals: 77
  panel_of_tumors: 0