Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/6f8ea6ffd0612b6b13155d2405592b/aih-tih-sc-c8485b-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/1627170c60e36c58472104d655238c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/1627170c60e36c58472104d655238c/.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: 186
  Pass (FILTER=PASS): 9 (4.8%)
  Fail (FILTER=FAIL): 177 (95.2%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 62
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 21
  confidence_below_min(low<high): 14
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 12
  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): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(0.0<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(medium<high);total_reads_below_min(5.0<8.0): 3
  total_reads_below_min(5.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 2

Breakdown by confidence:
  high: 9 pass, 3 fail (total: 12)
  low: 0 pass, 67 fail (total: 67)
  medium: 0 pass, 107 fail (total: 107)
Arriba filter: 186 rows -> 9 PASS; wrote aih-tih-sc-c8485b-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-c8485b-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-c8485b-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt