Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/58772abc22d7a11c300b4debe17c85/aih-tih-sc-2798bb-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/3eb41a68939881a22eb42c6661288b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/3eb41a68939881a22eb42c6661288b/.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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 225
  Pass (FILTER=PASS): 12 (5.3%)
  Fail (FILTER=FAIL): 213 (94.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 76
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 21
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 14
  confidence_below_min(low<high): 13
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3
  total_reads_below_min(4.0<8.0): 2
  total_reads_below_min(3.0<8.0): 2
  confidence_below_min(low<high);aih_curated_blacklist: 2

Breakdown by confidence:
  high: 12 pass, 5 fail (total: 17)
  low: 0 pass, 87 fail (total: 87)
  medium: 0 pass, 121 fail (total: 121)
Arriba filter: 225 rows -> 12 PASS; wrote aih-tih-sc-2798bb-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-2798bb-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-2798bb-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt