Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/703130db8fcffc8cfe29e9f45f516f/aih-tih-sc-550807-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/20c214c614fc20226d68350e3f24fb/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/20c214c614fc20226d68350e3f24fb/.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: 263
  Pass (FILTER=PASS): 35 (13.3%)
  Fail (FILTER=FAIL): 228 (86.7%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 40
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 35
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 21
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 19
  confidence_below_min(low<high): 17
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  total_reads_below_min(6.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4

Breakdown by confidence:
  high: 35 pass, 16 fail (total: 51)
  low: 0 pass, 106 fail (total: 106)
  medium: 0 pass, 106 fail (total: 106)
Arriba filter: 263 rows -> 35 PASS; wrote aih-tih-sc-550807-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-550807-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-550807-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt