Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/6d5a626eb4b5b1c5f681d065e0f7de/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/d7492a2ada10186d683de6b6e37e90/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/d7492a2ada10186d683de6b6e37e90/.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-f79a17a0-988d-46c3-a0fc-cc7f26b06d9c/2f/783d5e3fc4bb0e4fc378bb3e8b5e61/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 12 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 365
  Pass (FILTER=PASS): 63 (17.3%)
  Fail (FILTER=FAIL): 302 (82.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 12
  All 12 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 62
  confidence_below_min(medium<high): 58
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 24
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 20
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 20
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 19
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(low<high): 12
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 4

Breakdown by confidence:
  high: 63 pass, 6 fail (total: 69)
  low: 0 pass, 164 fail (total: 164)
  medium: 0 pass, 132 fail (total: 132)
Arriba filter: 365 rows -> 63 PASS; wrote SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.arriba.fusions.filtered.tsv and SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.arriba.fusions.filter_summary.txt