Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/5a1f003e588603f457086de7e7a86c/HCC1395_BL.CHIP_PON.merged.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/96f946cbce2504cc51cf08e39ceb1e/.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/cohort_blacklist.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/96f946cbce2504cc51cf08e39ceb1e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/5a1f003e588603f457086de7e7a86c/HCC1395_BL.CHIP_PON.merged.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CHIP/gene_family_blacklist.bed.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CHIP/encode_blacklist.bed.gz
==> STAGING COMPLETE (8 inputs)

[INFO] Loading resources...
[INFO] Cohort blacklist: 68611 positions
[INFO] Gene-family blacklist: 76473 positions
[INFO] ENCODE blacklist: 636 intervals
[INFO] Gene tiers: 19423 genes, max_tier=2
[INFO] Pre-filter: 0 PASS, 254 FAIL, 254 total
[INFO] Survivors BED: 0 sites written to HCC1395_BL.survivors.bed
[INFO]   no_functional_impact: 185
[INFO]   hard_filter_reject: 46
[INFO]   cohort_blacklist: 17
[INFO]   gene_not_in_universe: 5
[INFO]   pon_artifact: 1