Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/05cd9052f985933d5248cf6f5ec422/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/cf839325eb5113c5fca680a06150ca/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/05cd9052f985933d5248cf6f5ec422/.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 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 193
  Pass (FILTER=PASS): 4 (2.1%)
  Fail (FILTER=FAIL): 189 (97.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 51
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 14
  confidence_below_min(low<high): 11
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 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(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  aih_curated_blacklist: 1

Breakdown by confidence:
  high: 4 pass, 5 fail (total: 9)
  low: 0 pass, 85 fail (total: 85)
  medium: 0 pass, 99 fail (total: 99)
Arriba filter: 193 rows -> 4 PASS; wrote 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filtered.tsv and 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filter_summary.txt