Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/a85307c11766928af50b022d14d40a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/a85307c11766928af50b022d14d40a/.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/91/161badbdaedd3cd66bd7561778eeb3/FFPE_HD789_01_RNA_0004_B23LG7FLT4_1.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 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 323
  Pass (FILTER=PASS): 52 (16.1%)
  Fail (FILTER=FAIL): 271 (83.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 50
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 37
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 28
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 19
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 14
  confidence_below_min(low<high): 14
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 5

Breakdown by confidence:
  high: 52 pass, 8 fail (total: 60)
  low: 0 pass, 116 fail (total: 116)
  medium: 0 pass, 147 fail (total: 147)
Arriba filter: 323 rows -> 52 PASS; wrote FFPE_HD789_01_RNA_0004_B23LG7FLT4_1.arriba.fusions.filtered.tsv and FFPE_HD789_01_RNA_0004_B23LG7FLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_HD789_01_RNA_0004_B23LG7FLT4_1.arriba.fusions.filter_summary.txt