Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/b14f27232cf871c4c560d7b4e921fd/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/e9f190edf36313a8182eb655cb56d8/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/b14f27232cf871c4c560d7b4e921fd/.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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 274
  Pass (FILTER=PASS): 21 (7.7%)
  Fail (FILTER=FAIL): 253 (92.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 107
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 26
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 25
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 12
  confidence_below_min(low<high): 12
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3

Breakdown by confidence:
  high: 21 pass, 3 fail (total: 24)
  low: 0 pass, 91 fail (total: 91)
  medium: 0 pass, 159 fail (total: 159)
Arriba filter: 274 rows -> 21 PASS; wrote aih-tih-sc-a8a787-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-a8a787-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-a8a787-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt