Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/3ff520a2b83997498cd6b5e8046836/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/0783578b9440c6bccc22d7433f86c4/SkinN_FFPE_L09_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/3ff520a2b83997498cd6b5e8046836/.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 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 27
  Pass (FILTER=PASS): 2 (7.4%)
  Fail (FILTER=FAIL): 25 (92.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 4
  All 4 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high): 7
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(medium<high): 2
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 1
  confidence_below_min(low<high);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 1

Breakdown by confidence:
  high: 2 pass, 0 fail (total: 2)
  low: 0 pass, 20 fail (total: 20)
  medium: 0 pass, 5 fail (total: 5)
Arriba filter: 27 rows -> 2 PASS; wrote SkinN_FFPE_L09_RNA_01_B23LG7FLT4_1.arriba.fusions.filtered.tsv and SkinN_FFPE_L09_RNA_01_B23LG7FLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: SkinN_FFPE_L09_RNA_01_B23LG7FLT4_1.arriba.fusions.filter_summary.txt