Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/fe7225c895c5b4399fdf1a5e1c6b89/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/fe7225c895c5b4399fdf1a5e1c6b89/.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/9b/5679c535a455624559142d399af288/MCF7_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 691
  Pass (FILTER=PASS): 155 (22.4%)
  Fail (FILTER=FAIL): 536 (77.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 143
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 103
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 31
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 30
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 29
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 26
  confidence_below_min(low<high): 26
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 25
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 17
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 5

Breakdown by confidence:
  high: 155 pass, 10 fail (total: 165)
  low: 0 pass, 240 fail (total: 240)
  medium: 0 pass, 286 fail (total: 286)
Arriba filter: 691 rows -> 155 PASS; wrote MCF7_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.filtered.tsv and MCF7_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.filtered_pass_only.tsv
Summary written to: MCF7_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.filter_summary.txt