Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/a93c96433cdf43c65c30a7b559d373/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/a93c96433cdf43c65c30a7b559d373/.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/43/f76f51ac3a85e6f7660ee9115032c5/NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.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 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 298
  Pass (FILTER=PASS): 66 (22.1%)
  Fail (FILTER=FAIL): 232 (77.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 4
  All 4 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 67
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 40
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 17
  confidence_below_min(low<high): 17
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 15
  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): 10
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  total_reads_below_min(3.0<8.0): 2

Breakdown by confidence:
  high: 66 pass, 6 fail (total: 72)
  low: 0 pass, 119 fail (total: 119)
  medium: 0 pass, 107 fail (total: 107)
Arriba filter: 298 rows -> 66 PASS; wrote NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.filtered.tsv and NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.filtered_pass_only.tsv
Summary written to: NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.filter_summary.txt