Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/cfa300e47a3823d97e919de5f5a987/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/cfa300e47a3823d97e919de5f5a987/.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/c8/123e88b22ad73e259256ef440d3004/aih-tih-sc-c35cc3-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 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 186
  Pass (FILTER=PASS): 19 (10.2%)
  Fail (FILTER=FAIL): 167 (89.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 62
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 17
  confidence_below_min(low<high): 13
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0);aih_curated_blacklist: 2
  total_reads_below_min(6.0<8.0): 2
  confidence_below_min(medium<high);aih_curated_blacklist: 2

Breakdown by confidence:
  high: 19 pass, 3 fail (total: 22)
  low: 0 pass, 73 fail (total: 73)
  medium: 0 pass, 91 fail (total: 91)
Arriba filter: 186 rows -> 19 PASS; wrote aih-tih-sc-c35cc3-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-c35cc3-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-c35cc3-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt