Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/abbbbadb71bed9322ca42da8d845bf/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/abbbbadb71bed9322ca42da8d845bf/.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/e2/7dbaebe61c666951518eead669cfb5/BVT_FFPE_TRNA_liv_03_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 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 79
  Pass (FILTER=PASS): 21 (26.6%)
  Fail (FILTER=FAIL): 58 (73.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(medium<high): 5
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(low<high): 2
  aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 1
  confidence_below_min(low<high);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 21 pass, 1 fail (total: 22)
  low: 0 pass, 32 fail (total: 32)
  medium: 0 pass, 25 fail (total: 25)
Arriba filter: 79 rows -> 21 PASS; wrote BVT_FFPE_TRNA_liv_03_A23WKFTLT4_2.arriba.fusions.filtered.tsv and BVT_FFPE_TRNA_liv_03_A23WKFTLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: BVT_FFPE_TRNA_liv_03_A23WKFTLT4_2.arriba.fusions.filter_summary.txt