Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/0a614f4c494b1689ba304f64e73699/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/0a614f4c494b1689ba304f64e73699/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/ac39d8ea370fca620b2bea7961756d/FFPE_V4_0002_RNA_0001_B23WHYVLT4_1.arriba.fusions.tsv
  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-8900cb43-4dca-49ac-a290-1d176a2e0012/49/8453bafeca2d0250d89cdefd7ba73e/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 152
  Pass (FILTER=PASS): 19 (12.5%)
  Fail (FILTER=FAIL): 133 (87.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 25
  confidence_below_min(low<high): 23
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  aih_curated_blacklist: 1
  total_reads_below_min(4.0<8.0): 1

Breakdown by confidence:
  high: 19 pass, 3 fail (total: 22)
  low: 0 pass, 87 fail (total: 87)
  medium: 0 pass, 43 fail (total: 43)
Arriba filter: 152 rows -> 19 PASS; wrote FFPE_V4_0002_RNA_0001_B23WHYVLT4_1.arriba.fusions.filtered.tsv and FFPE_V4_0002_RNA_0001_B23WHYVLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_V4_0002_RNA_0001_B23WHYVLT4_1.arriba.fusions.filter_summary.txt