Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/fe4a6ba2c52b314c0b558c8f2fcfb6/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/fe4a6ba2c52b314c0b558c8f2fcfb6/.command.sh
  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/6d/c3db2b1e4d98cd5f1171b5678de401/BVT_FFPE_TRNA_bst_05_A23WKFTLT4_2.arriba.fusions.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 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 337
  Pass (FILTER=PASS): 61 (18.1%)
  Fail (FILTER=FAIL): 276 (81.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 50
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 36
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 27
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 27
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 26
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 25
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(low<high): 7
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 5
  total_reads_below_min(7.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 4

Breakdown by confidence:
  high: 61 pass, 20 fail (total: 81)
  low: 0 pass, 109 fail (total: 109)
  medium: 0 pass, 147 fail (total: 147)
Arriba filter: 337 rows -> 61 PASS; wrote BVT_FFPE_TRNA_bst_05_A23WKFTLT4_2.arriba.fusions.filtered.tsv and BVT_FFPE_TRNA_bst_05_A23WKFTLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: BVT_FFPE_TRNA_bst_05_A23WKFTLT4_2.arriba.fusions.filter_summary.txt