Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/9b697ffa79a53dd66558a95bc2f5ca/BVT_FFPE_TRNA_utn_02_A23WKFTLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/3740cfef4a74d1f338bc50009008d9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/3740cfef4a74d1f338bc50009008d9/.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 13 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 192
  Pass (FILTER=PASS): 9 (4.7%)
  Fail (FILTER=FAIL): 183 (95.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 13
  All 13 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 56
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 15
  confidence_below_min(low<high): 11
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  total_reads_below_min(4.0<8.0): 2

Breakdown by confidence:
  high: 9 pass, 2 fail (total: 11)
  low: 0 pass, 73 fail (total: 73)
  medium: 0 pass, 108 fail (total: 108)
Arriba filter: 192 rows -> 9 PASS; wrote BVT_FFPE_TRNA_utn_02_A23WKFTLT4_1.arriba.fusions.filtered.tsv and BVT_FFPE_TRNA_utn_02_A23WKFTLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: BVT_FFPE_TRNA_utn_02_A23WKFTLT4_1.arriba.fusions.filter_summary.txt