Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/2cd06faf9e58b7af054d19a14fb62d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/2cd06faf9e58b7af054d19a14fb62d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/4f2c7eed2cef6a19554515f06e509b/aih-tih-sc-693ffe-R1_A23WJ53LT4_1.arriba.fusions.tsv
  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 2 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 204
  Pass (FILTER=PASS): 26 (12.7%)
  Fail (FILTER=FAIL): 178 (87.3%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 24
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 19
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 17
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 11
  confidence_below_min(low<high): 5
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  total_reads_below_min(6.0<8.0): 3
  total_reads_below_min(3.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 3

Breakdown by confidence:
  high: 26 pass, 10 fail (total: 36)
  low: 0 pass, 68 fail (total: 68)
  medium: 0 pass, 100 fail (total: 100)
Arriba filter: 204 rows -> 26 PASS; wrote aih-tih-sc-693ffe-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-693ffe-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt