Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/60a0cbb7b5bf451c6df950b6a7e580/BT-20_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/01cc44a1dfd8b0c8203cb1bfe90e73/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/01cc44a1dfd8b0c8203cb1bfe90e73/.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 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 40
  Pass (FILTER=PASS): 0 (0.0%)
  Fail (FILTER=FAIL): 40 (100.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 4
  All 4 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 5
  confidence_below_min(medium<high): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high): 3
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  low: 0 pass, 12 fail (total: 12)
  medium: 0 pass, 28 fail (total: 28)
Arriba filter: 40 rows -> 0 PASS; wrote BT-20_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.filtered.tsv and BT-20_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: BT-20_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.filter_summary.txt