Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/0ec4811c0fad29e5483704fde05d65/FFPE_V4_0002_RNA_0001_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/d1fdd661c05a3f3c1a0c4eafe05e2b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/d1fdd661c05a3f3c1a0c4eafe05e2b/.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-6a8e5f46-8592-47ae-b09e-a1efe7f02cb2/6a/80a8f8c27f6b00a3a33e35ea914965/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 76
  Pass (FILTER=PASS): 19 (25.0%)
  Fail (FILTER=FAIL): 57 (75.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high): 9
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(medium<high): 6
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0);aih_curated_blacklist: 2
  total_reads_below_min(7.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 1

Breakdown by confidence:
  high: 19 pass, 1 fail (total: 20)
  low: 0 pass, 42 fail (total: 42)
  medium: 0 pass, 14 fail (total: 14)
Arriba filter: 76 rows -> 19 PASS; wrote FFPE_V4_0002_RNA_0001_B23WHTKLT4_1.arriba.fusions.filtered.tsv and FFPE_V4_0002_RNA_0001_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_V4_0002_RNA_0001_B23WHTKLT4_1.arriba.fusions.filter_summary.txt