Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/20e12bb7b2fd91fc68cad1195a78e4/aih-tih-sc-4e749e-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/87161ba852fdfebe0e2de4dd4e9e6f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/87161ba852fdfebe0e2de4dd4e9e6f/.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 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 169
  Pass (FILTER=PASS): 8 (4.7%)
  Fail (FILTER=FAIL): 161 (95.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 10
  All 10 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 50
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 21
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2
  total_reads_below_min(4.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 8 pass, 1 fail (total: 9)
  low: 0 pass, 62 fail (total: 62)
  medium: 0 pass, 98 fail (total: 98)
Arriba filter: 169 rows -> 8 PASS; wrote aih-tih-sc-4e749e-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-4e749e-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt