Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/03a85b575c56a0e778526d7b7c075f/aih-tih-sc-64fc89-R1_A23YTGFLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/b65c33eebcd6fc14532208b47d1793/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/b65c33eebcd6fc14532208b47d1793/.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 15 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 1101
  Pass (FILTER=PASS): 40 (3.6%)
  Fail (FILTER=FAIL): 1061 (96.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 15
  All 15 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 430
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 89
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 79
  confidence_below_min(medium<high): 71
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 66
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 52
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 47
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 46
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 46
  confidence_below_min(low<high): 33
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 10

Breakdown by confidence:
  high: 40 pass, 6 fail (total: 46)
  low: 0 pass, 668 fail (total: 668)
  medium: 0 pass, 387 fail (total: 387)
Arriba filter: 1101 rows -> 40 PASS; wrote aih-tih-sc-64fc89-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-64fc89-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-64fc89-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt