Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/a21529d12e1ad9649e480093961c9a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/a21529d12e1ad9649e480093961c9a/.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/06/8b8c8da2ec83ea261c8a90d8d5cfa5/aih-tih-sc-6cc13c-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 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 393
  Pass (FILTER=PASS): 27 (6.9%)
  Fail (FILTER=FAIL): 366 (93.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 94
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 86
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 25
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 25
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 22
  confidence_below_min(low<high): 22
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 3

Breakdown by confidence:
  high: 27 pass, 5 fail (total: 32)
  low: 0 pass, 205 fail (total: 205)
  medium: 0 pass, 156 fail (total: 156)
Arriba filter: 393 rows -> 27 PASS; wrote aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt