Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/7fbd96ae9600b03f59d8d1c0ee2383/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/7fbd96ae9600b03f59d8d1c0ee2383/.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/41/6980c01b610fddad55f517f279fb3b/aih-tih-sc-58b830-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 2 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 101
  Pass (FILTER=PASS): 1 (1.0%)
  Fail (FILTER=FAIL): 100 (99.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 2
  All 2 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 43
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 6
  confidence_below_min(low<high): 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  total_reads_below_min(4.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(medium<high);aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 1
  confidence_below_min(low<high);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 1

Breakdown by confidence:
  high: 1 pass, 2 fail (total: 3)
  low: 0 pass, 31 fail (total: 31)
  medium: 0 pass, 67 fail (total: 67)
Arriba filter: 101 rows -> 1 PASS; wrote aih-tih-sc-58b830-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-58b830-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-58b830-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt