Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/ec7753034fce549d558606f195952b/SkinN_FFPE_L07_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/385ec28532c01a2f0dd7e368e49830/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/385ec28532c01a2f0dd7e368e49830/.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 1 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 5
  Pass (FILTER=PASS): 0 (0.0%)
  Fail (FILTER=FAIL): 5 (100.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 1
  All 1 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 2
  confidence_below_min(low<high): 1
  confidence_below_min(low<high);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 1

Breakdown by confidence:
  low: 0 pass, 3 fail (total: 3)
  medium: 0 pass, 2 fail (total: 2)
Arriba filter: 5 rows -> 0 PASS; wrote SkinN_FFPE_L07_RNA_01_B23LG7FLT4_1.arriba.fusions.filtered.tsv and SkinN_FFPE_L07_RNA_01_B23LG7FLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: SkinN_FFPE_L07_RNA_01_B23LG7FLT4_1.arriba.fusions.filter_summary.txt