Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/b868ccb13a8e00b2ca6cc85016f3e7/aih-tih-sc-66e7f5-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/76cad0afc9f41d6e5e2ae76e50aadb/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/76cad0afc9f41d6e5e2ae76e50aadb/.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 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 112
  Pass (FILTER=PASS): 7 (6.2%)
  Fail (FILTER=FAIL): 105 (93.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 4
  All 4 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 30
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(medium<high): 5
  total_reads_below_min(3.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(low<high): 3
  total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 1

Breakdown by confidence:
  high: 7 pass, 7 fail (total: 14)
  low: 0 pass, 24 fail (total: 24)
  medium: 0 pass, 74 fail (total: 74)
Arriba filter: 112 rows -> 7 PASS; wrote aih-tih-sc-66e7f5-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-66e7f5-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-66e7f5-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt