Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/7d19c164d4da545e7c24e93bc21434/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/7d19c164d4da545e7c24e93bc21434/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/eec57b694837d95b85f872d77fdfa9/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-0d61fb92-10f8-436b-b82d-72e6736f5100/c4/183e6190d93d4c9e85fb7eb5e7e8c4/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: 25
  Pass (FILTER=PASS): 13 (52.0%)
  Fail (FILTER=FAIL): 12 (48.0%)

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

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

Breakdown by confidence:
  high: 13 pass, 0 fail (total: 13)
  low: 0 pass, 5 fail (total: 5)
  medium: 0 pass, 7 fail (total: 7)
Arriba filter: 25 rows -> 13 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