Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/cf3dbe95f1b8050ffec7b4a8c5735e/1173_HOB_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/3c96663c2a5e50a1aec60c6754e4a9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/3c96663c2a5e50a1aec60c6754e4a9/.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-fe242a7f-c5b9-4d3f-88fa-f3e739280d3a/0e/64006b836d7933c012afba79f66ebb/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 13 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 174
  Pass (FILTER=PASS): 9 (5.2%)
  Fail (FILTER=FAIL): 165 (94.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 13
  All 13 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 75
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 11
  confidence_below_min(low<high): 11
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2
  confidence_below_min(low<high);aih_curated_blacklist: 2
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 1

Breakdown by confidence:
  high: 9 pass, 2 fail (total: 11)
  low: 0 pass, 69 fail (total: 69)
  medium: 0 pass, 94 fail (total: 94)
Arriba filter: 174 rows -> 9 PASS; wrote 1173_HOB_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filtered.tsv and 1173_HOB_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 1173_HOB_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filter_summary.txt