Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/39ffecc84a12d5793c98dcaedcf7b2/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/39ffecc84a12d5793c98dcaedcf7b2/.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/38/746fa25eb031c8eaee5bf50103ec3a/ColoN_FFPE_L01_RNA_01_B23LG7FLT4_2.arriba.fusions.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 2 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 15
  Pass (FILTER=PASS): 0 (0.0%)
  Fail (FILTER=FAIL): 15 (100.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 2
  All 2 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 4
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 2
  confidence_below_min(medium<high);aih_curated_blacklist: 1
  confidence_below_min(low<high): 1
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  low: 0 pass, 10 fail (total: 10)
  medium: 0 pass, 5 fail (total: 5)
Arriba filter: 15 rows -> 0 PASS; wrote ColoN_FFPE_L01_RNA_01_B23LG7FLT4_2.arriba.fusions.filtered.tsv and ColoN_FFPE_L01_RNA_01_B23LG7FLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: ColoN_FFPE_L01_RNA_01_B23LG7FLT4_2.arriba.fusions.filter_summary.txt