Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/13651baecc7e289ae17e317561cc74/MCF7_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/e071392ff33a78bbe46a429165f6e7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/e071392ff33a78bbe46a429165f6e7/.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-f79a17a0-988d-46c3-a0fc-cc7f26b06d9c/2f/783d5e3fc4bb0e4fc378bb3e8b5e61/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 732
  Pass (FILTER=PASS): 155 (21.2%)
  Fail (FILTER=FAIL): 577 (78.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 138
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 83
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 50
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 45
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 33
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 31
  confidence_below_min(low<high): 30
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 25
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 23
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(4.0<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(5.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 7

Breakdown by confidence:
  high: 155 pass, 20 fail (total: 175)
  low: 0 pass, 233 fail (total: 233)
  medium: 0 pass, 324 fail (total: 324)
Arriba filter: 732 rows -> 155 PASS; wrote MCF7_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.filtered.tsv and MCF7_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: MCF7_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.filter_summary.txt