Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/792eeb190a808e4b2e693dbfc1674b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/792eeb190a808e4b2e693dbfc1674b/.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/61/6cdd636f1cad5a3844bf7be541b5a3/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.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 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 472
  Pass (FILTER=PASS): 61 (12.9%)
  Fail (FILTER=FAIL): 411 (87.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 109
  confidence_below_min(medium<high): 74
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 26
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 26
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 23
  confidence_below_min(low<high): 22
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 20
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 20
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 6

Breakdown by confidence:
  high: 61 pass, 9 fail (total: 70)
  low: 0 pass, 251 fail (total: 251)
  medium: 0 pass, 151 fail (total: 151)
Arriba filter: 472 rows -> 61 PASS; wrote Hs746T_FFPE_RNA_0001_23LG7FLT4_1.arriba.fusions.filtered.tsv and Hs746T_FFPE_RNA_0001_23LG7FLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: Hs746T_FFPE_RNA_0001_23LG7FLT4_1.arriba.fusions.filter_summary.txt