Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/9f28ec60de32493b4c8c6c65f67e7a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/9f28ec60de32493b4c8c6c65f67e7a/.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/48/8d9c2a64054426a0b473544045c4aa/dna_s770.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-fff52061-f714-4c14-bb2c-bf5549840817/43/06b80417dcdedb0d1513f19552f633/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: 78
  Pass (FILTER=PASS): 1 (1.3%)
  Fail (FILTER=FAIL): 77 (98.7%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 32
  confidence_below_min(low<high): 10
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 2
  total_reads_below_min(3.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(medium<high);aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 1

Breakdown by confidence:
  high: 1 pass, 1 fail (total: 2)
  low: 0 pass, 33 fail (total: 33)
  medium: 0 pass, 43 fail (total: 43)
Arriba filter: 78 rows -> 1 PASS; wrote dna_s770.arriba.fusions.filtered.tsv and dna_s770.arriba.fusions.filtered_pass_only.tsv
Summary written to: dna_s770.arriba.fusions.filter_summary.txt