Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/a53d1199d4e81a1bf0524e53cae6e0/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CHIP/gene_tiers.tsv
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CHIP/cosmic_heme.tsv.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CHIP/cohort_blacklist.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/a53d1199d4e81a1bf0524e53cae6e0/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/0523eecc2ed07cb6a58fbafdba6721/Sig_18_Blood.readcount_annotated.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/0523eecc2ed07cb6a58fbafdba6721/Sig_18_Blood.readcount_annotated.vcf.gz
==> STAGING COMPLETE (7 inputs)

[INFO] Scoring params: TLOD>=60, blood:tumor>=2.0
[INFO] Blacklist: 68611 positions
[INFO] COSMIC heme: 113942 variants
[INFO] Gene tiers: 19423 genes
[INFO] Pass 1: Reading and scoring variants...
[INFO] Read 321 variants
[INFO] Pass 2: Writing scored variants...
[INFO] Scored: 0 CHIP_PASS, 321 CHIP_FAIL, 321 total