Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/2a283d2dd2b6f40d3d9c1b23d10e72/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/f72ddc1b9a523dc59a5212c93592d1/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/2a283d2dd2b6f40d3d9c1b23d10e72/.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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 173
  Pass (FILTER=PASS): 28 (16.2%)
  Fail (FILTER=FAIL): 145 (83.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 31
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high): 8
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3
  total_reads_below_min(5.0<8.0): 2
  total_reads_below_min(3.0<8.0): 2
  total_reads_below_min(3.0<8.0);aih_curated_blacklist: 2

Breakdown by confidence:
  high: 28 pass, 6 fail (total: 34)
  low: 0 pass, 66 fail (total: 66)
  medium: 0 pass, 73 fail (total: 73)
Arriba filter: 173 rows -> 28 PASS; wrote BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.arriba.fusions.filtered.tsv and BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.arriba.fusions.filter_summary.txt