Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/5574e09d2cecf86988ebd24bc3599c/BVT_FFPE_TRNA_utn_05_A23WKFTLT4_3.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/f3dd75535b997a19b446c73d43a14d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/f3dd75535b997a19b446c73d43a14d/.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 2 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 46
  Pass (FILTER=PASS): 11 (23.9%)
  Fail (FILTER=FAIL): 35 (76.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 2
  All 2 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(medium<high): 2
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 1
  total_reads_below_min(7.0<8.0): 1
  total_reads_below_min(5.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 1
  confidence_below_min(low<high): 1
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 1

Breakdown by confidence:
  high: 11 pass, 2 fail (total: 13)
  low: 0 pass, 15 fail (total: 15)
  medium: 0 pass, 18 fail (total: 18)
Arriba filter: 46 rows -> 11 PASS; wrote BVT_FFPE_TRNA_utn_05_A23WKFTLT4_3.arriba.fusions.filtered.tsv and BVT_FFPE_TRNA_utn_05_A23WKFTLT4_3.arriba.fusions.filtered_pass_only.tsv
Summary written to: BVT_FFPE_TRNA_utn_05_A23WKFTLT4_3.arriba.fusions.filter_summary.txt