Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/0e86606dc51b5b6d8852306301b86d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/0e86606dc51b5b6d8852306301b86d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/14c1c5ea13dbe778df248a2c7d6086/rna_s1221_S42.arriba.fusions.tsv
  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-b770051b-a87c-42e4-a930-dadf721dd5e0/6c/f32ee62dd2afb437c98c7d18ce4297/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: 29
  Pass (FILTER=PASS): 9 (31.0%)
  Fail (FILTER=FAIL): 20 (69.0%)

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

Failure reasons (top 15):
  total_reads_below_min(6.0<8.0): 5
  confidence_below_min(medium<high): 3
  confidence_below_min(low<high): 3
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(medium<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(0.0<8.0): 1

Breakdown by confidence:
  high: 9 pass, 5 fail (total: 14)
  low: 0 pass, 11 fail (total: 11)
  medium: 0 pass, 4 fail (total: 4)
Arriba filter: 29 rows -> 9 PASS; wrote rna_s1221_S42.arriba.fusions.filtered.tsv and rna_s1221_S42.arriba.fusions.filtered_pass_only.tsv
Summary written to: rna_s1221_S42.arriba.fusions.filter_summary.txt