Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/972f805e7a0102fc6da136e8685082/BVT_FFPE_TRNA_stm_07_A23WKFTLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/c41c6d0fc2499c29af5c1c89cc4278/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/c41c6d0fc2499c29af5c1c89cc4278/.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: 283
  Pass (FILTER=PASS): 27 (9.5%)
  Fail (FILTER=FAIL): 256 (90.5%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 62
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 39
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 14
  confidence_below_min(low<high): 14
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3
  total_reads_below_min(6.0<8.0): 3

Breakdown by confidence:
  high: 27 pass, 9 fail (total: 36)
  low: 0 pass, 116 fail (total: 116)
  medium: 0 pass, 131 fail (total: 131)
Arriba filter: 283 rows -> 27 PASS; wrote BVT_FFPE_TRNA_stm_07_A23WKFTLT4_1.arriba.fusions.filtered.tsv and BVT_FFPE_TRNA_stm_07_A23WKFTLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: BVT_FFPE_TRNA_stm_07_A23WKFTLT4_1.arriba.fusions.filter_summary.txt