Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/e2e45f6f70f586ae92dc7760d6b5f2/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/e2e45f6f70f586ae92dc7760d6b5f2/.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/a6/16e1f7481615f0f188f2fbf73053a4/BVT_FFPE_TRNA_thy_02_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 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 182
  Pass (FILTER=PASS): 6 (3.3%)
  Fail (FILTER=FAIL): 176 (96.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 10
  All 10 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 69
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(low<high): 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3
  total_reads_below_min(7.0<8.0): 2

Breakdown by confidence:
  high: 6 pass, 4 fail (total: 10)
  low: 0 pass, 51 fail (total: 51)
  medium: 0 pass, 121 fail (total: 121)
Arriba filter: 182 rows -> 6 PASS; wrote BVT_FFPE_TRNA_thy_02_A23WKFTLT4_2.arriba.fusions.filtered.tsv and BVT_FFPE_TRNA_thy_02_A23WKFTLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: BVT_FFPE_TRNA_thy_02_A23WKFTLT4_2.arriba.fusions.filter_summary.txt