Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/860a36ac1367933d11ce3c5bdfbd06/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/860a36ac1367933d11ce3c5bdfbd06/.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/31/1c91e3f533cf5200c00a47df1e9fe3/BT-20_FFPE_RNA_0001_B23LG7FLT4_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 2 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 42
  Pass (FILTER=PASS): 1 (2.4%)
  Fail (FILTER=FAIL): 41 (97.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 2
  All 2 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(medium<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(medium<high): 2
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 2
  confidence_below_min(low<high): 1
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 1

Breakdown by confidence:
  high: 1 pass, 0 fail (total: 1)
  low: 0 pass, 7 fail (total: 7)
  medium: 0 pass, 34 fail (total: 34)
Arriba filter: 42 rows -> 1 PASS; wrote BT-20_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filtered.tsv and BT-20_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filter_summary.txt