Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/9735ee00d45e6ed9ebceb6c5cedece/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/9735ee00d45e6ed9ebceb6c5cedece/.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/bb/4057ec611849f457c91166c94c1c25/659_Mt-T1-TRNA-1_A23MVY2LT4_1.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 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 190
  Pass (FILTER=PASS): 6 (3.2%)
  Fail (FILTER=FAIL): 184 (96.8%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 58
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 30
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 24
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 14
  confidence_below_min(low<high): 11
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  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): 4
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  total_reads_below_min(4.0<8.0): 2
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 2

Breakdown by confidence:
  high: 6 pass, 4 fail (total: 10)
  low: 0 pass, 78 fail (total: 78)
  medium: 0 pass, 102 fail (total: 102)
Arriba filter: 190 rows -> 6 PASS; wrote 659_Mt-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filtered.tsv and 659_Mt-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_Mt-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filter_summary.txt