Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/c8c03813f1f59eecbf28af406c8152/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/c8c03813f1f59eecbf28af406c8152/.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/d8/851e0ebe44b79a879ad8631b6b0802/BVT_FFPE_TRNA_crv_01_A23WKFTLT4_1.arriba.fusions.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 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 290
  Pass (FILTER=PASS): 20 (6.9%)
  Fail (FILTER=FAIL): 270 (93.1%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 84
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 57
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 27
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(low<high): 9
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 1

Breakdown by confidence:
  high: 20 pass, 3 fail (total: 23)
  low: 0 pass, 111 fail (total: 111)
  medium: 0 pass, 156 fail (total: 156)
Arriba filter: 290 rows -> 20 PASS; wrote BVT_FFPE_TRNA_crv_01_A23WKFTLT4_1.arriba.fusions.filtered.tsv and BVT_FFPE_TRNA_crv_01_A23WKFTLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: BVT_FFPE_TRNA_crv_01_A23WKFTLT4_1.arriba.fusions.filter_summary.txt