Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/5e6c28f5b46a3b964fcd6b0f3877e7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/860036a28a21e5f01706afeab9c54f/659_d01-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/5e6c28f5b46a3b964fcd6b0f3877e7/.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 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 168
  Pass (FILTER=PASS): 7 (4.2%)
  Fail (FILTER=FAIL): 161 (95.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 43
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 30
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 12
  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(low<high): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0);aih_curated_blacklist: 2

Breakdown by confidence:
  high: 7 pass, 2 fail (total: 9)
  low: 0 pass, 84 fail (total: 84)
  medium: 0 pass, 75 fail (total: 75)
Arriba filter: 168 rows -> 7 PASS; wrote 659_d01-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered.tsv and 659_d01-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_d01-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filter_summary.txt