Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/5bbdfe83294bdb4fd08223ab96d6e1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/5bbdfe83294bdb4fd08223ab96d6e1/.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/63/cfa38ca5deef2650ee90601f6fa475/659_ecd-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-bba2394f-ea06-4038-829e-f0bb41c45b0f/84/e510984b93930338ae941c5c84bcbe/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 12 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 533
  Pass (FILTER=PASS): 72 (13.5%)
  Fail (FILTER=FAIL): 461 (86.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 12
  All 12 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 143
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 51
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 43
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 38
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 24
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 22
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 17
  confidence_below_min(low<high): 16
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 7
  total_reads_below_min(4.0<8.0): 6

Breakdown by confidence:
  high: 72 pass, 23 fail (total: 95)
  low: 0 pass, 180 fail (total: 180)
  medium: 0 pass, 258 fail (total: 258)
Arriba filter: 533 rows -> 72 PASS; wrote 659_ecd-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered.tsv and 659_ecd-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_ecd-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filter_summary.txt