Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/10302c83425aca04534c623e731490/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/10302c83425aca04534c623e731490/.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/e2/7d518b85a3ce8a231aa7658084bc31/aih-tih-sc-b6a2e8-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 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 256
  Pass (FILTER=PASS): 26 (10.2%)
  Fail (FILTER=FAIL): 230 (89.8%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 70
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 25
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 19
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 18
  confidence_below_min(low<high): 17
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 6
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 4
  total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 4

Breakdown by confidence:
  high: 26 pass, 6 fail (total: 32)
  low: 0 pass, 82 fail (total: 82)
  medium: 0 pass, 142 fail (total: 142)
Arriba filter: 256 rows -> 26 PASS; wrote aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt