Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/8b8ca6b35fba062a6f70e47c56d2a8/SW780_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/53e120178a81ef35c786463e6b56ec/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/53e120178a81ef35c786463e6b56ec/.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 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 440
  Pass (FILTER=PASS): 72 (16.4%)
  Fail (FILTER=FAIL): 368 (83.6%)

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): 78
  confidence_below_min(medium<high): 58
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 38
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 24
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 21
  confidence_below_min(low<high): 21
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 5

Breakdown by confidence:
  high: 72 pass, 10 fail (total: 82)
  low: 0 pass, 206 fail (total: 206)
  medium: 0 pass, 152 fail (total: 152)
Arriba filter: 440 rows -> 72 PASS; wrote SW780_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.filtered.tsv and SW780_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: SW780_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.filter_summary.txt