Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/f063d4a268ff1bad42e2c17098fa60/.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/e7/f063d4a268ff1bad42e2c17098fa60/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/3d01ba9fcdffd2b147e93bf6318b05/positive_somatic_control_1.snv_indel.annotated.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/3d01ba9fcdffd2b147e93bf6318b05/positive_somatic_control_1.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: 173 variants processed, 0 PASS
  low_tumor_dp: 38
  low_normal_dp: 173
  low_tumor_alt: 43
  high_normal_vaf: 105
  panel_of_normals: 61
  panel_of_tumors: 0