Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/d476bf8746412fdd56d3c153b33938/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/d476bf8746412fdd56d3c153b33938/.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/c2/fac11796bbd571f2b7094340061037/BVT_FFPE_TRNA_thy_02_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 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 186
  Pass (FILTER=PASS): 20 (10.8%)
  Fail (FILTER=FAIL): 166 (89.2%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 72
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high): 8
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3
  aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 1
  total_reads_below_min(5.0<8.0): 1

Breakdown by confidence:
  high: 20 pass, 3 fail (total: 23)
  low: 0 pass, 67 fail (total: 67)
  medium: 0 pass, 96 fail (total: 96)
Arriba filter: 186 rows -> 20 PASS; wrote BVT_FFPE_TRNA_thy_02_A23WKFTLT4_1.arriba.fusions.filtered.tsv and BVT_FFPE_TRNA_thy_02_A23WKFTLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: BVT_FFPE_TRNA_thy_02_A23WKFTLT4_1.arriba.fusions.filter_summary.txt