Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/b3975e576d6db8bbbf9e76980e0358/aih-tih-sc-9ab390-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/aa762ea85c95f4c0ef05fbdc5791ed/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/aa762ea85c95f4c0ef05fbdc5791ed/.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-5ae5f7b1-ce8a-4a12-9374-820c751df9c5/09/a7ecdb27117590dd6e7bf9e221420e/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 145
  Pass (FILTER=PASS): 9 (6.2%)
  Fail (FILTER=FAIL): 136 (93.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 26
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 26
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 10
  confidence_below_min(low<high): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  total_reads_below_min(3.0<8.0);aih_curated_blacklist: 2
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 1
  aih_curated_blacklist: 1

Breakdown by confidence:
  high: 9 pass, 4 fail (total: 13)
  low: 0 pass, 55 fail (total: 55)
  medium: 0 pass, 77 fail (total: 77)
Arriba filter: 145 rows -> 9 PASS; wrote aih-tih-sc-9ab390-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-9ab390-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-9ab390-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt