Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/77e886eb7d242a737b8fce5d05bf39/aih-tih-sc-318819-R1_A23YTGFLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/e5a7a4d389cad2e128115632d3ccd9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/e5a7a4d389cad2e128115632d3ccd9/.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 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 132
  Pass (FILTER=PASS): 2 (1.5%)
  Fail (FILTER=FAIL): 130 (98.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 24
  confidence_below_min(low<high): 14
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 7
  confidence_below_min(medium<high): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2
  total_reads_below_min(4.0<8.0): 1

Breakdown by confidence:
  high: 2 pass, 1 fail (total: 3)
  low: 0 pass, 60 fail (total: 60)
  medium: 0 pass, 69 fail (total: 69)
Arriba filter: 132 rows -> 2 PASS; wrote aih-tih-sc-318819-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-318819-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-318819-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt