Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/346747a262cd505b5d5fa4da78836f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/346747a262cd505b5d5fa4da78836f/.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/5a/a69bf30060f8f1158f6b366077429f/aih-tih-sc-6832bb-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-5ae5f7b1-ce8a-4a12-9374-820c751df9c5/09/a7ecdb27117590dd6e7bf9e221420e/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 12 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 254
  Pass (FILTER=PASS): 40 (15.7%)
  Fail (FILTER=FAIL): 214 (84.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 12
  All 12 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 83
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 21
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 17
  confidence_below_min(low<high): 16
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2

Breakdown by confidence:
  high: 40 pass, 1 fail (total: 41)
  low: 0 pass, 101 fail (total: 101)
  medium: 0 pass, 112 fail (total: 112)
Arriba filter: 254 rows -> 40 PASS; wrote aih-tih-sc-6832bb-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-6832bb-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-6832bb-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt