Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/54215f86b67c7fa2e89f82f65732b5/659_epP-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/c5dfd953bc2531ca44fd071da58f5d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/c5dfd953bc2531ca44fd071da58f5d/.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-bba2394f-ea06-4038-829e-f0bb41c45b0f/84/e510984b93930338ae941c5c84bcbe/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 143
  Pass (FILTER=PASS): 9 (6.3%)
  Fail (FILTER=FAIL): 134 (93.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 10
  All 10 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 21
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 18
  confidence_below_min(medium<high): 17
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 9
  confidence_below_min(low<high): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 3
  total_reads_below_min(3.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0);aih_curated_blacklist: 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2
  aih_curated_blacklist: 1

Breakdown by confidence:
  high: 9 pass, 5 fail (total: 14)
  low: 0 pass, 77 fail (total: 77)
  medium: 0 pass, 52 fail (total: 52)
Arriba filter: 143 rows -> 9 PASS; wrote 659_epP-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered.tsv and 659_epP-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_epP-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filter_summary.txt