Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/067a6c8b699c25143ef2b14572cd62/1173_LAF_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/20e4c80a87167b5c92caea23cd5333/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/20e4c80a87167b5c92caea23cd5333/.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 2 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 48
  Pass (FILTER=PASS): 0 (0.0%)
  Fail (FILTER=FAIL): 48 (100.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 2
  All 2 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 25
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 5
  confidence_below_min(low<high): 3
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 3
  total_reads_below_min(4.0<8.0): 2
  confidence_below_min(medium<high);aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 0 pass, 2 fail (total: 2)
  low: 0 pass, 13 fail (total: 13)
  medium: 0 pass, 33 fail (total: 33)
Arriba filter: 48 rows -> 0 PASS; wrote 1173_LAF_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filtered.tsv and 1173_LAF_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 1173_LAF_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filter_summary.txt