Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/03ef8b1082e56ad5201c8ae8befb0c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/03ef8b1082e56ad5201c8ae8befb0c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/de0fc992b4edd6048721e1bea670d2/659_bua-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv
  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 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 170
  Pass (FILTER=PASS): 16 (9.4%)
  Fail (FILTER=FAIL): 154 (90.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 27
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 26
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 19
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(low<high): 5
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  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(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  aih_curated_blacklist: 2
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0);aih_curated_blacklist: 2

Breakdown by confidence:
  high: 16 pass, 5 fail (total: 21)
  low: 0 pass, 79 fail (total: 79)
  medium: 0 pass, 70 fail (total: 70)
Arriba filter: 170 rows -> 16 PASS; wrote 659_bua-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered.tsv and 659_bua-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_bua-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filter_summary.txt