Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/1d1520e01a78bd9484d79ba43f68cf/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/1d1520e01a78bd9484d79ba43f68cf/.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/98/a87fef1d1d5156db1819eb309955d5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-e543dae6-5fea-4720-bfb6-150bf1ff20d4/33/a04540cea7c8abc13163bc03b147d5/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 16 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 430
  Pass (FILTER=PASS): 62 (14.4%)
  Fail (FILTER=FAIL): 368 (85.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 16
  All 16 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 76
  confidence_below_min(medium<high): 63
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 32
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 30
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 22
  confidence_below_min(low<high): 21
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 5

Breakdown by confidence:
  high: 62 pass, 5 fail (total: 67)
  low: 0 pass, 195 fail (total: 195)
  medium: 0 pass, 168 fail (total: 168)
Arriba filter: 430 rows -> 62 PASS; wrote FFPE_HD789_01_RNA_13_A23YTGFLT4_1.arriba.fusions.filtered.tsv and FFPE_HD789_01_RNA_13_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.arriba.fusions.filter_summary.txt