Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/ff252216bcd12421b7c5b7e33c49f2/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/22f37dae4aee3698e3ffefdf74dd0d/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_3.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/ff252216bcd12421b7c5b7e33c49f2/.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 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 404
  Pass (FILTER=PASS): 67 (16.6%)
  Fail (FILTER=FAIL): 337 (83.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 10
  All 10 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 91
  confidence_below_min(medium<high): 57
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 26
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 19
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 19
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 10
  confidence_below_min(low<high): 10
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4

Breakdown by confidence:
  high: 67 pass, 7 fail (total: 74)
  low: 0 pass, 192 fail (total: 192)
  medium: 0 pass, 138 fail (total: 138)
Arriba filter: 404 rows -> 67 PASS; wrote SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_3.arriba.fusions.filtered.tsv and SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_3.arriba.fusions.filtered_pass_only.tsv
Summary written to: SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_3.arriba.fusions.filter_summary.txt