Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/526c2b675a581bb9129e11d7271b22/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/9b863b250451cfb94f43f53447b6aa/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/9b863b250451cfb94f43f53447b6aa/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/blacklist_breakpoint_database_2026-04-27.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-6ef41cd9-2e18-4687-842c-3f6f49c5643f/f2/edcdb43d4676ed2a5254ed1bf31faa/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 8 fusion rows (breakpoint_ID in qualified set)

================================================================================
ARRIBA FILTERING SUMMARY
================================================================================

Total fusions: 389
  Pass (FILTER=PASS): 65 (16.7%)
  Fail (FILTER=FAIL): 324 (83.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 70
  confidence_below_min(medium<high): 61
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 33
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 20
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 19
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 11
  confidence_below_min(low<high): 11
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 5
  total_reads_below_min(3.0<8.0): 4

Breakdown by confidence:
  high: 65 pass, 12 fail (total: 77)
  low: 0 pass, 174 fail (total: 174)
  medium: 0 pass, 138 fail (total: 138)
Arriba filter: 389 rows -> 65 PASS; wrote SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.arriba.fusions.filtered.tsv and SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.arriba.fusions.filter_summary.txt