Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/9b933576f7cd8001583e0a275403a5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/9b933576f7cd8001583e0a275403a5/.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/b0/f10c2f307988433bc4cf89916e347c/aih-tih-sc-c400f1-R1_A23YTGFLT4_1.arriba.fusions.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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 221
  Pass (FILTER=PASS): 21 (9.5%)
  Fail (FILTER=FAIL): 200 (90.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 39
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 22
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 19
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 17
  confidence_below_min(low<high): 14
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 2

Breakdown by confidence:
  high: 21 pass, 4 fail (total: 25)
  low: 0 pass, 96 fail (total: 96)
  medium: 0 pass, 100 fail (total: 100)
Arriba filter: 221 rows -> 21 PASS; wrote aih-tih-sc-c400f1-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-c400f1-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-c400f1-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt