Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/f9d342c72ab02c98dea18f96b4e5e6/rna_s1200_S21.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/05acfe748859b37787f79e8b26bb60/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/05acfe748859b37787f79e8b26bb60/.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-b770051b-a87c-42e4-a930-dadf721dd5e0/6c/f32ee62dd2afb437c98c7d18ce4297/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: 29
  Pass (FILTER=PASS): 6 (20.7%)
  Fail (FILTER=FAIL): 23 (79.3%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(low<high): 3
  total_reads_below_min(7.0<8.0): 2
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 2
  total_reads_below_min(6.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 1

Breakdown by confidence:
  high: 6 pass, 3 fail (total: 9)
  low: 0 pass, 10 fail (total: 10)
  medium: 0 pass, 10 fail (total: 10)
Arriba filter: 29 rows -> 6 PASS; wrote rna_s1200_S21.arriba.fusions.filtered.tsv and rna_s1200_S21.arriba.fusions.filtered_pass_only.tsv
Summary written to: rna_s1200_S21.arriba.fusions.filter_summary.txt