Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/1e581f6471537e4c138f4e7dd2a209/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/1e581f6471537e4c138f4e7dd2a209/.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/c1/97fa28ea52b660106f3931a14aee52/659_Mt-T1-TRNA-1_A23MVY2LT4_2.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 3 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 152
  Pass (FILTER=PASS): 5 (3.3%)
  Fail (FILTER=FAIL): 147 (96.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 3
  All 3 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 36
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 25
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 7
  confidence_below_min(low<high): 6
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2

Breakdown by confidence:
  high: 5 pass, 2 fail (total: 7)
  low: 0 pass, 75 fail (total: 75)
  medium: 0 pass, 70 fail (total: 70)
Arriba filter: 152 rows -> 5 PASS; wrote 659_Mt-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered.tsv and 659_Mt-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_Mt-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filter_summary.txt