Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/4beeef7561e559a12847bcd3f66452/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/60b0670bf396b776895de5560f968b/HCC1395_BL.germline.harmonized.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CHIP/cosmic_heme.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/a4f5c26b74015c788ab972d924e413/HCC1395_tumor_vs_HCC1395_BL.snv_indel.phased.vep.final.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/4beeef7561e559a12847bcd3f66452/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/94344acf5316550d6e11c4a4a1ba38/HCC1395_BL.scored.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/94344acf5316550d6e11c4a4a1ba38/HCC1395_BL.scored.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/60b0670bf396b776895de5560f968b/HCC1395_BL.germline.harmonized.vcf.gz
==> STAGING COMPLETE (8 inputs)

[INFO] Deconfliction mode: CHIP↔Germline, CHIP↔Somatic, Germline↔Somatic
[INFO] COSMIC heme: 113942 variants
[INFO] Building germline lookup...
[INFO] Germline lookup: 354 variants
[INFO] Building somatic lookup...
[INFO] Somatic lookup: 6 variants
[INFO] Processing CHIP VCF (Phase 1, pass 1: scoring decisions)...
[INFO] Processing CHIP VCF (Phase 1, pass 2: writing)...
[INFO] Writing deconflicted germline VCF...
[INFO] Germline: 0 variants suppressed
[INFO] Writing deconflicted somatic VCF...
[INFO] Somatic: 0 variants suppressed

[INFO] === Deconfliction Summary ===
  CHIP variants processed:
    CHIP_PASS no conflict:   0
    CHIP ↔ Germline:         0
      → CHIP wins:           0
      → Germline wins:       0
      → Suppressed (grey):   0
    CHIP ↔ Somatic (suspect):0
    CHIP_FAIL pass-through:  254
    Multihit cap:            0
  Germline ↔ Somatic:        0
    → Germline wins:         0
    → Suppress both:         0
  Audit TSV: HCC1395_BL.deconfliction_audit.tsv