Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/d99da4cd57a0fccc9e14aeef35b686/U118MG_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/0066c99c66d2e65e5e310956502c7c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/0066c99c66d2e65e5e310956502c7c/.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-6ef41cd9-2e18-4687-842c-3f6f49c5643f/f2/edcdb43d4676ed2a5254ed1bf31faa/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: 371
  Pass (FILTER=PASS): 52 (14.0%)
  Fail (FILTER=FAIL): 319 (86.0%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 94
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 49
  confidence_below_min(low<high): 25
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 6
  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

Breakdown by confidence:
  high: 52 pass, 10 fail (total: 62)
  low: 0 pass, 155 fail (total: 155)
  medium: 0 pass, 154 fail (total: 154)
Arriba filter: 371 rows -> 52 PASS; wrote U118MG_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filtered.tsv and U118MG_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: U118MG_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filter_summary.txt