Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/5a624a12f43da90ee8ba67abaaebdc/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/4437c35e11e269952b8a7fe3e84d41/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/4437c35e11e269952b8a7fe3e84d41/.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-eb5d3959-7137-45a9-9f26-41f9201dcf7f/81/be38f7f47cc30e4a107d9e602cb8fb/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 314
  Pass (FILTER=PASS): 39 (12.4%)
  Fail (FILTER=FAIL): 275 (87.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 68
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 32
  confidence_below_min(low<high): 30
  confidence_below_min(medium<high): 27
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3

Breakdown by confidence:
  high: 39 pass, 10 fail (total: 49)
  low: 0 pass, 159 fail (total: 159)
  medium: 0 pass, 106 fail (total: 106)
Arriba filter: 314 rows -> 39 PASS; wrote aih-tih-sc-b8457f-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-b8457f-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-b8457f-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt