Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/70f2bd4f562dbd8a8d550d71b2b6d8/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/70f2bd4f562dbd8a8d550d71b2b6d8/.command.sh
  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/ab/2fd19ba75124e8283f3b55744fc3dc/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.arriba.fusions.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 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 450
  Pass (FILTER=PASS): 38 (8.4%)
  Fail (FILTER=FAIL): 412 (91.6%)

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

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 150
  confidence_below_min(medium<high): 69
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 29
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 28
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 27
  confidence_below_min(low<high): 19
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3

Breakdown by confidence:
  high: 38 pass, 3 fail (total: 41)
  low: 0 pass, 244 fail (total: 244)
  medium: 0 pass, 165 fail (total: 165)
Arriba filter: 450 rows -> 38 PASS; wrote aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt