Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/a31c02815418582158572a7e8ed534/659_6i-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/81ca6a5539d73978a97f1e10b07906/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/81ca6a5539d73978a97f1e10b07906/.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-6a8e5f46-8592-47ae-b09e-a1efe7f02cb2/6a/80a8f8c27f6b00a3a33e35ea914965/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 59
  Pass (FILTER=PASS): 4 (6.8%)
  Fail (FILTER=FAIL): 55 (93.2%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 4
  All 4 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(medium<high): 11
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2
  confidence_below_min(low<high): 2
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 2
  total_reads_below_min(4.0<8.0): 1
  total_reads_below_min(3.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 1

Breakdown by confidence:
  high: 4 pass, 2 fail (total: 6)
  low: 0 pass, 21 fail (total: 21)
  medium: 0 pass, 32 fail (total: 32)
Arriba filter: 59 rows -> 4 PASS; wrote 659_6i-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered.tsv and 659_6i-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_6i-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filter_summary.txt