Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/849b4778b4ff4181b21b09620cad42/BVT_FFPE_TRNA_thy_02_A23WKFTLT4_3.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/5bb1e2176f9ca7211af71b68b7c6e9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/5bb1e2176f9ca7211af71b68b7c6e9/.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-13dfb8f7-c999-4ef0-9260-22ba79cf647d/75/c52a23060671398a8253a658f32ecc/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: 126
  Pass (FILTER=PASS): 5 (4.0%)
  Fail (FILTER=FAIL): 121 (96.0%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 40
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 24
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 2
  total_reads_below_min(7.0<8.0);aih_curated_blacklist: 1
  total_reads_below_min(4.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 1

Breakdown by confidence:
  high: 5 pass, 2 fail (total: 7)
  low: 0 pass, 35 fail (total: 35)
  medium: 0 pass, 84 fail (total: 84)
Arriba filter: 126 rows -> 5 PASS; wrote BVT_FFPE_TRNA_thy_02_A23WKFTLT4_3.arriba.fusions.filtered.tsv and BVT_FFPE_TRNA_thy_02_A23WKFTLT4_3.arriba.fusions.filtered_pass_only.tsv
Summary written to: BVT_FFPE_TRNA_thy_02_A23WKFTLT4_3.arriba.fusions.filter_summary.txt