Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/cf5e175bde3fb222a7b6a5cd943f76/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/cf5e175bde3fb222a7b6a5cd943f76/.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/f5/ed3e5eb109475fdccc23133dde8b05/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.arriba.fusions.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: 145
  Pass (FILTER=PASS): 15 (10.3%)
  Fail (FILTER=FAIL): 130 (89.7%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 47
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 10
  confidence_below_min(low<high): 8
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 2
  total_reads_below_min(6.0<8.0): 1

Breakdown by confidence:
  high: 15 pass, 2 fail (total: 17)
  low: 0 pass, 45 fail (total: 45)
  medium: 0 pass, 83 fail (total: 83)
Arriba filter: 145 rows -> 15 PASS; wrote aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt