Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/f20bd7a458ac8d8436fcabeab066e0/U118MG_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/02235c6106d08fa053cc965c130197/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/02235c6106d08fa053cc965c130197/.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 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 398
  Pass (FILTER=PASS): 57 (14.3%)
  Fail (FILTER=FAIL): 341 (85.7%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 92
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 76
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 31
  confidence_below_min(low<high): 18
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 4

Breakdown by confidence:
  high: 57 pass, 5 fail (total: 62)
  low: 0 pass, 171 fail (total: 171)
  medium: 0 pass, 165 fail (total: 165)
Arriba filter: 398 rows -> 57 PASS; wrote U118MG_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.filtered.tsv and U118MG_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: U118MG_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.filter_summary.txt