Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/3367835cad7bcd292f086854ec514b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/2703b38465ea918d5946efd5d6da13/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/3367835cad7bcd292f086854ec514b/.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 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 315
  Pass (FILTER=PASS): 34 (10.8%)
  Fail (FILTER=FAIL): 281 (89.2%)

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): 36
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 36
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 30
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 17
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 16
  confidence_below_min(low<high): 16
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  total_reads_below_min(6.0<8.0): 2

Breakdown by confidence:
  high: 34 pass, 4 fail (total: 38)
  low: 0 pass, 165 fail (total: 165)
  medium: 0 pass, 112 fail (total: 112)
Arriba filter: 315 rows -> 34 PASS; wrote aih-tih-sc-5519ab-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-5519ab-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-5519ab-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt