Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/c9faea5e15df35d9dfe8436052a258/BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/15aa7513a20d3bcb9f960b2f28070b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/15aa7513a20d3bcb9f960b2f28070b/.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-13dfb8f7-c999-4ef0-9260-22ba79cf647d/75/c52a23060671398a8253a658f32ecc/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 15 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 378
  Pass (FILTER=PASS): 70 (18.5%)
  Fail (FILTER=FAIL): 308 (81.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 15
  All 15 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 75
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 36
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 25
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 24
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 15
  confidence_below_min(low<high): 13
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 5

Breakdown by confidence:
  high: 70 pass, 13 fail (total: 83)
  low: 0 pass, 120 fail (total: 120)
  medium: 0 pass, 175 fail (total: 175)
Arriba filter: 378 rows -> 70 PASS; wrote BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.arriba.fusions.filtered.tsv and BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.arriba.fusions.filter_summary.txt