Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/67390b8142a5bc11a32792ffc787e3/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/ef9b1adad4963f41b582ad6c6cde05/aih-tih-sc-9be8d4-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/67390b8142a5bc11a32792ffc787e3/.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: 236
  Pass (FILTER=PASS): 51 (21.6%)
  Fail (FILTER=FAIL): 185 (78.4%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 46
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 24
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 23
  confidence_below_min(low<high): 16
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(medium<high);aih_curated_blacklist: 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  total_reads_below_min(6.0<8.0): 2
  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(low<high);total_reads_below_min(6.0<8.0): 1

Breakdown by confidence:
  high: 51 pass, 9 fail (total: 60)
  low: 0 pass, 102 fail (total: 102)
  medium: 0 pass, 74 fail (total: 74)
Arriba filter: 236 rows -> 51 PASS; wrote aih-tih-sc-9be8d4-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-9be8d4-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-9be8d4-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt