Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/579414fa11a21eb2d283fa10efb5c8/659_gK-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/331d0a9445ea4a90ddc9898de19982/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/331d0a9445ea4a90ddc9898de19982/.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 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 114
  Pass (FILTER=PASS): 11 (9.6%)
  Fail (FILTER=FAIL): 103 (90.4%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 16
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 8
  confidence_below_min(low<high): 7
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 1
  aih_curated_blacklist: 1

Breakdown by confidence:
  high: 11 pass, 4 fail (total: 15)
  low: 0 pass, 61 fail (total: 61)
  medium: 0 pass, 38 fail (total: 38)
Arriba filter: 114 rows -> 11 PASS; wrote 659_gK-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered.tsv and 659_gK-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_gK-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filter_summary.txt