Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/5d645c9f5446ad74f2d7e9b6baf4ff/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/5d645c9f5446ad74f2d7e9b6baf4ff/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/c82d141232595ca9eaed8c66761ea5/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-7b3818c0-d4ea-4c00-9f17-cd6e279eadc4/42/1d60ae12b95e36ba907a0f1fa7897f/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