Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/b76b4d3b2591eaa75e81b74cf4985d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/b76b4d3b2591eaa75e81b74cf4985d/.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/29/8dfd712cbacff2827042e78bc58889/FFPE_V4_0002_RNA_0001_A23T55JLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-fe242a7f-c5b9-4d3f-88fa-f3e739280d3a/0e/64006b836d7933c012afba79f66ebb/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 131
  Pass (FILTER=PASS): 19 (14.5%)
  Fail (FILTER=FAIL): 112 (85.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 12
  confidence_below_min(medium<high): 11
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 11
  confidence_below_min(low<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(4.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2
  aih_curated_blacklist: 1
  total_reads_below_min(6.0<8.0): 1

Breakdown by confidence:
  high: 19 pass, 3 fail (total: 22)
  low: 0 pass, 82 fail (total: 82)
  medium: 0 pass, 27 fail (total: 27)
Arriba filter: 131 rows -> 19 PASS; wrote FFPE_V4_0002_RNA_0001_A23T55JLT4_1.arriba.fusions.filtered.tsv and FFPE_V4_0002_RNA_0001_A23T55JLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_V4_0002_RNA_0001_A23T55JLT4_1.arriba.fusions.filter_summary.txt