Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/42943bb362d6a001e3de534d83b00e/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/9bd36dc111139dd25b1dc2208a896e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/9bd36dc111139dd25b1dc2208a896e/.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 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 244
  Pass (FILTER=PASS): 26 (10.7%)
  Fail (FILTER=FAIL): 218 (89.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 10
  All 10 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 65
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 35
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 25
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 17
  confidence_below_min(low<high): 14
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 6
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3

Breakdown by confidence:
  high: 26 pass, 6 fail (total: 32)
  low: 0 pass, 88 fail (total: 88)
  medium: 0 pass, 124 fail (total: 124)
Arriba filter: 244 rows -> 26 PASS; wrote 1173_M5U_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filtered.tsv and 1173_M5U_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 1173_M5U_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filter_summary.txt