Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/f8a9fd32ae3f291036663655fd7a42/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/f8a9fd32ae3f291036663655fd7a42/.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/bd/01fab80eb55c913acd325094151e4f/tih_rna_sample_00480_B23WHTKLT4_2.arriba.fusions.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 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 308
  Pass (FILTER=PASS): 62 (20.1%)
  Fail (FILTER=FAIL): 246 (79.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 31
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 31
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 22
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 20
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 19
  confidence_below_min(low<high): 18
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 9
  total_reads_below_min(5.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  total_reads_below_min(4.0<8.0): 4
  total_reads_below_min(3.0<8.0): 4

Breakdown by confidence:
  high: 62 pass, 20 fail (total: 82)
  low: 0 pass, 107 fail (total: 107)
  medium: 0 pass, 119 fail (total: 119)
Arriba filter: 308 rows -> 62 PASS; wrote tih_rna_sample_00480_B23WHTKLT4_2.arriba.fusions.filtered.tsv and tih_rna_sample_00480_B23WHTKLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00480_B23WHTKLT4_2.arriba.fusions.filter_summary.txt