Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/ee91b8a1a01303b945871b87a5e0c9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/ee91b8a1a01303b945871b87a5e0c9/.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/03/1ae77b7b9045885020608a6a9583ce/U118MG_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-f79a17a0-988d-46c3-a0fc-cc7f26b06d9c/2f/783d5e3fc4bb0e4fc378bb3e8b5e61/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: 400
  Pass (FILTER=PASS): 54 (13.5%)
  Fail (FILTER=FAIL): 346 (86.5%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 98
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 59
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 26
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 23
  confidence_below_min(low<high): 17
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 4

Breakdown by confidence:
  high: 54 pass, 10 fail (total: 64)
  low: 0 pass, 160 fail (total: 160)
  medium: 0 pass, 176 fail (total: 176)
Arriba filter: 400 rows -> 54 PASS; wrote U118MG_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.filtered.tsv and U118MG_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.filtered_pass_only.tsv
Summary written to: U118MG_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.filter_summary.txt