Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/bcfe114dafba50dc02d38f96c8c584/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/bcfe114dafba50dc02d38f96c8c584/.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/12/5b34e9bea86ab1f67839ab618e8588/PX_FFPE_pan_TRNA_nat_03_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 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 190
  Pass (FILTER=PASS): 8 (4.2%)
  Fail (FILTER=FAIL): 182 (95.8%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 61
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<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

Breakdown by confidence:
  high: 8 pass, 4 fail (total: 12)
  low: 0 pass, 70 fail (total: 70)
  medium: 0 pass, 108 fail (total: 108)
Arriba filter: 190 rows -> 8 PASS; wrote PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1.arriba.fusions.filtered.tsv and PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1.arriba.fusions.filter_summary.txt