Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/54c1b605028b4fa2c1814616594863/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/54c1b605028b4fa2c1814616594863/.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/4b/0b8e4d8075c8b3144ac645a3a93a82/BVT_FFPE_TRNA_utn_05_A23WKFTLT4_2.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: 73
  Pass (FILTER=PASS): 12 (16.4%)
  Fail (FILTER=FAIL): 61 (83.6%)

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(6.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(low<high): 6
  confidence_below_min(medium<high): 5
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 2
  total_reads_below_min(6.0<8.0): 1
  total_reads_below_min(5.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 12 pass, 2 fail (total: 14)
  low: 0 pass, 28 fail (total: 28)
  medium: 0 pass, 31 fail (total: 31)
Arriba filter: 73 rows -> 12 PASS; wrote BVT_FFPE_TRNA_utn_05_A23WKFTLT4_2.arriba.fusions.filtered.tsv and BVT_FFPE_TRNA_utn_05_A23WKFTLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: BVT_FFPE_TRNA_utn_05_A23WKFTLT4_2.arriba.fusions.filter_summary.txt