Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/29791c2e08ebc554876425f4b313ac/aih-tih-sc-64fc89-R1_A23YTGFLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/32100403ae598f940aba3a7d5017be/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/32100403ae598f940aba3a7d5017be/.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-e543dae6-5fea-4720-bfb6-150bf1ff20d4/33/a04540cea7c8abc13163bc03b147d5/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 15 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 1101
  Pass (FILTER=PASS): 40 (3.6%)
  Fail (FILTER=FAIL): 1061 (96.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 15
  All 15 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 430
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 89
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 79
  confidence_below_min(medium<high): 71
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 66
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 52
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 47
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 46
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 46
  confidence_below_min(low<high): 33
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 10

Breakdown by confidence:
  high: 40 pass, 6 fail (total: 46)
  low: 0 pass, 668 fail (total: 668)
  medium: 0 pass, 387 fail (total: 387)
Arriba filter: 1101 rows -> 40 PASS; wrote aih-tih-sc-64fc89-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-64fc89-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-64fc89-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt