Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/44c93f24d17aa27a3f13499a925580/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/bac884d63aa577fc165f3fa238bbc2/.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/c3/bac884d63aa577fc165f3fa238bbc2/.command.run
  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 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 207
  Pass (FILTER=PASS): 38 (18.4%)
  Fail (FILTER=FAIL): 169 (81.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 67
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 15
  confidence_below_min(low<high): 13
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2
  confidence_below_min(low<high);aih_curated_blacklist: 1
  aih_curated_blacklist: 1

Breakdown by confidence:
  high: 38 pass, 3 fail (total: 41)
  low: 0 pass, 71 fail (total: 71)
  medium: 0 pass, 95 fail (total: 95)
Arriba filter: 207 rows -> 38 PASS; wrote aih-tih-sc-fe8311-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-fe8311-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-fe8311-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt