Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/f13f091364b219f62d208ba65ca4a9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/f13f091364b219f62d208ba65ca4a9/.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/1f/9010465883ed65594835a29871b83d/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.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 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 123
  Pass (FILTER=PASS): 19 (15.4%)
  Fail (FILTER=FAIL): 104 (84.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 11
  confidence_below_min(low<high): 10
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 8
  confidence_below_min(medium<high): 8
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 2
  aih_curated_blacklist: 1

Breakdown by confidence:
  high: 19 pass, 3 fail (total: 22)
  low: 0 pass, 76 fail (total: 76)
  medium: 0 pass, 25 fail (total: 25)
Arriba filter: 123 rows -> 19 PASS; wrote FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.arriba.fusions.filtered.tsv and FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.arriba.fusions.filter_summary.txt