Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/151cb7c745796f8866b62ce9c918e0/FFPE_HD789_02_RNA_0014_B23MHV2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/00ba43f904e72e36879f4471c2ed7b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/00ba43f904e72e36879f4471c2ed7b/.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-40cc52c0-5bec-40b6-b04d-c64c51f55eff/cf/a844d18c3db3aeda7471fb3d005c4f/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 13 fusion rows (breakpoint_ID in qualified set)

================================================================================
ARRIBA FILTERING SUMMARY
================================================================================

Total fusions: 453
  Pass (FILTER=PASS): 64 (14.1%)
  Fail (FILTER=FAIL): 389 (85.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 13
  All 13 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 103
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 64
  confidence_below_min(low<high): 30
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 20
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 19
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 17
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 6

Breakdown by confidence:
  high: 64 pass, 9 fail (total: 73)
  low: 0 pass, 196 fail (total: 196)
  medium: 0 pass, 184 fail (total: 184)
Arriba filter: 453 rows -> 64 PASS; wrote FFPE_HD789_02_RNA_0014_B23MHV2LT4_1.arriba.fusions.filtered.tsv and FFPE_HD789_02_RNA_0014_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_HD789_02_RNA_0014_B23MHV2LT4_1.arriba.fusions.filter_summary.txt