Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/461e7fae852755d3add43ab891fc44/1136_5WB-N1-BDNA-1_B23KFG5LT4_1.CHIP_PON.merged.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/c142390cd1401229976b708dcaa6b6/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/461e7fae852755d3add43ab891fc44/1136_5WB-N1-BDNA-1_B23KFG5LT4_1.CHIP_PON.merged.vcf.gz.tbi
  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/9f/c142390cd1401229976b708dcaa6b6/.command.run
  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: 3 PASS, 27826 FAIL, 27829 total
[INFO] Survivors BED: 3 sites written to 1136_5WB-N1-BDNA-1_B23KFG5LT4_1.survivors.bed
[INFO]   no_functional_impact: 18604
[INFO]   hard_filter_reject: 7121
[INFO]   cohort_blacklist: 1337
[INFO]   gene_not_in_universe: 556
[INFO]   pon_artifact: 152
[INFO]   gene_family_blacklist: 51
[INFO]   encode_blacklist: 5