Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/d65929343fee951870cee5ce9bd2c2/659_eHw-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/ccdf7947da84ec25c9440ec3a6a96b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/ccdf7947da84ec25c9440ec3a6a96b/.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 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 149
  Pass (FILTER=PASS): 6 (4.0%)
  Fail (FILTER=FAIL): 143 (96.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 74
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 3
  total_reads_below_min(4.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(6.0<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(1.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 6 pass, 3 fail (total: 9)
  low: 0 pass, 44 fail (total: 44)
  medium: 0 pass, 96 fail (total: 96)
Arriba filter: 149 rows -> 6 PASS; wrote 659_eHw-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered.tsv and 659_eHw-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_eHw-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filter_summary.txt