Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/9f2a32b300a473556b013c2ded14a4/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/34d616713803679083edc334eb9a66/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/34d616713803679083edc334eb9a66/.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-6ef41cd9-2e18-4687-842c-3f6f49c5643f/f2/edcdb43d4676ed2a5254ed1bf31faa/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: 6
  Pass (FILTER=PASS): 0 (0.0%)
  Fail (FILTER=FAIL): 6 (100.0%)

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

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

Breakdown by confidence:
  high: 0 pass, 1 fail (total: 1)
  low: 0 pass, 3 fail (total: 3)
  medium: 0 pass, 2 fail (total: 2)
Arriba filter: 6 rows -> 0 PASS; wrote SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.arriba.fusions.filtered.tsv and SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.arriba.fusions.filter_summary.txt