Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/de44dd4a1fe8b762d983e93eca799a/659_buD-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/9430122dc2a0141e8b734597ce9643/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/9430122dc2a0141e8b734597ce9643/.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 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 253
  Pass (FILTER=PASS): 45 (17.8%)
  Fail (FILTER=FAIL): 208 (82.2%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 31
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 31
  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): 23
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high): 10
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3

Breakdown by confidence:
  high: 45 pass, 7 fail (total: 52)
  low: 0 pass, 91 fail (total: 91)
  medium: 0 pass, 110 fail (total: 110)
Arriba filter: 253 rows -> 45 PASS; wrote 659_buD-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered.tsv and 659_buD-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_buD-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filter_summary.txt