Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/68c4db3a85b2d0994573e8235aa994/FFPE_V4_0001_RNA_0003_B23MHV2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/79759e99170606bd0240c234611fb4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/79759e99170606bd0240c234611fb4/.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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 148
  Pass (FILTER=PASS): 21 (14.2%)
  Fail (FILTER=FAIL): 127 (85.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 21
  confidence_below_min(low<high): 14
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(medium<high): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  aih_curated_blacklist: 1
  total_reads_below_min(4.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 1

Breakdown by confidence:
  high: 21 pass, 2 fail (total: 23)
  low: 0 pass, 103 fail (total: 103)
  medium: 0 pass, 22 fail (total: 22)
Arriba filter: 148 rows -> 21 PASS; wrote FFPE_V4_0001_RNA_0003_B23MHV2LT4_1.arriba.fusions.filtered.tsv and FFPE_V4_0001_RNA_0003_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_V4_0001_RNA_0003_B23MHV2LT4_1.arriba.fusions.filter_summary.txt