Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/6bd13538a9cb61f6dc9837aa900e74/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/6bd13538a9cb61f6dc9837aa900e74/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/ee599a95928aa1afa72c6dc82ca44e/RT4_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.tsv
  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: 211
  Pass (FILTER=PASS): 19 (9.0%)
  Fail (FILTER=FAIL): 192 (91.0%)

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(1.0<8.0): 45
  confidence_below_min(medium<high): 39
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(low<high): 12
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  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): 6
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4

Breakdown by confidence:
  high: 19 pass, 3 fail (total: 22)
  low: 0 pass, 113 fail (total: 113)
  medium: 0 pass, 76 fail (total: 76)
Arriba filter: 211 rows -> 19 PASS; wrote RT4_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.filtered.tsv and RT4_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: RT4_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.filter_summary.txt