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