Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/bce7cdcb55ff9c53abfeaa0ba786e5/659_ciJ-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/256a072e0576a08f4742719f5b52f4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/256a072e0576a08f4742719f5b52f4/.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 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 225
  Pass (FILTER=PASS): 26 (11.6%)
  Fail (FILTER=FAIL): 199 (88.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 87
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 9
  confidence_below_min(low<high): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 3
  aih_curated_blacklist: 1
  total_reads_below_min(7.0<8.0): 1

Breakdown by confidence:
  high: 26 pass, 3 fail (total: 29)
  low: 0 pass, 71 fail (total: 71)
  medium: 0 pass, 125 fail (total: 125)
Arriba filter: 225 rows -> 26 PASS; wrote 659_ciJ-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered.tsv and 659_ciJ-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_ciJ-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filter_summary.txt