Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/9d8efd2146c83348811d17b8b7c94e/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/382e4d732c8a7d9de56e9482b93c48/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/382e4d732c8a7d9de56e9482b93c48/.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 1 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 66
  Pass (FILTER=PASS): 9 (13.6%)
  Fail (FILTER=FAIL): 57 (86.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 1
  All 1 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(medium<high): 5
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 4
  total_reads_below_min(7.0<8.0): 2
  total_reads_below_min(4.0<8.0): 2
  confidence_below_min(low<high): 2
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  total_reads_below_min(6.0<8.0): 1
  total_reads_below_min(5.0<8.0): 1
  total_reads_below_min(3.0<8.0): 1
  total_reads_below_min(2.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 1

Breakdown by confidence:
  high: 9 pass, 8 fail (total: 17)
  low: 0 pass, 27 fail (total: 27)
  medium: 0 pass, 22 fail (total: 22)
Arriba filter: 66 rows -> 9 PASS; wrote BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.arriba.fusions.filtered.tsv and BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.arriba.fusions.filtered_pass_only.tsv
Summary written to: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.arriba.fusions.filter_summary.txt