Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/8db8f34333270100b59361cb6b59f6/786-O_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/9da72f273866bccd83ed7895c28740/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/9da72f273866bccd83ed7895c28740/.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/stage-6ef41cd9-2e18-4687-842c-3f6f49c5643f/f2/edcdb43d4676ed2a5254ed1bf31faa/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 298
  Pass (FILTER=PASS): 26 (8.7%)
  Fail (FILTER=FAIL): 272 (91.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 103
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 40
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 20
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(low<high): 13
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(5.0<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(6.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 4

Breakdown by confidence:
  high: 26 pass, 2 fail (total: 28)
  low: 0 pass, 127 fail (total: 127)
  medium: 0 pass, 143 fail (total: 143)
Arriba filter: 298 rows -> 26 PASS; wrote 786-O_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filtered.tsv and 786-O_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 786-O_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filter_summary.txt