Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/60022ef337482b72f6db63db63d8da/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/60022ef337482b72f6db63db63d8da/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/bf5431afc116672990e1358d6eac46/aih-tih-sc-714733-R1_A23YTGFLT4_1.arriba.fusions.tsv
  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 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 716
  Pass (FILTER=PASS): 123 (17.2%)
  Fail (FILTER=FAIL): 593 (82.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 144
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 119
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 55
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 47
  confidence_below_min(low<high): 36
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 23
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 23
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 8

Breakdown by confidence:
  high: 123 pass, 10 fail (total: 133)
  low: 0 pass, 264 fail (total: 264)
  medium: 0 pass, 319 fail (total: 319)
Arriba filter: 716 rows -> 123 PASS; wrote aih-tih-sc-714733-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-714733-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-714733-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt