Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/82734edd7e705de621608821bbd01e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/45fff44d6da2e59ffc96d8c27b68cf/BT-20_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/82734edd7e705de621608821bbd01e/.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 3 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 28
  Pass (FILTER=PASS): 0 (0.0%)
  Fail (FILTER=FAIL): 28 (100.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 3
  All 3 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 10
  confidence_below_min(low<high): 4
  confidence_below_min(medium<high): 3
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 2
  confidence_below_min(medium<high);aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(low<high);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 1

Breakdown by confidence:
  low: 0 pass, 21 fail (total: 21)
  medium: 0 pass, 7 fail (total: 7)
Arriba filter: 28 rows -> 0 PASS; wrote BT-20_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.filtered.tsv and BT-20_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.filtered_pass_only.tsv
Summary written to: BT-20_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.filter_summary.txt