Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/c94951437225df3327bb11ff5b9370/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/0ffa7c9669bdf860b803ed7b4f78f0/BVT_FFPE_TRNA_bst_04_A23WKFTLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/c94951437225df3327bb11ff5b9370/.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 3 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 367
  Pass (FILTER=PASS): 60 (16.3%)
  Fail (FILTER=FAIL): 307 (83.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 3
  All 3 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 80
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 45
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 34
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 29
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 17
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 9
  confidence_below_min(low<high): 8
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 7
  total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  total_reads_below_min(7.0<8.0): 3

Breakdown by confidence:
  high: 60 pass, 16 fail (total: 76)
  low: 0 pass, 119 fail (total: 119)
  medium: 0 pass, 172 fail (total: 172)
Arriba filter: 367 rows -> 60 PASS; wrote BVT_FFPE_TRNA_bst_04_A23WKFTLT4_1.arriba.fusions.filtered.tsv and BVT_FFPE_TRNA_bst_04_A23WKFTLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: BVT_FFPE_TRNA_bst_04_A23WKFTLT4_1.arriba.fusions.filter_summary.txt