Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/2fa86bbc44b9ab5c17e34cb12a3271/aih-tih-sc-8c7069-R1_A23YTGFLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/bccc36cddcf3d6f592c67e7eab461f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/bccc36cddcf3d6f592c67e7eab461f/.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 3 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 220
  Pass (FILTER=PASS): 32 (14.5%)
  Fail (FILTER=FAIL): 188 (85.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 3
  All 3 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 42
  confidence_below_min(low<high): 28
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 17
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  total_reads_below_min(5.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  total_reads_below_min(3.0<8.0): 3

Breakdown by confidence:
  high: 32 pass, 12 fail (total: 44)
  low: 0 pass, 78 fail (total: 78)
  medium: 0 pass, 98 fail (total: 98)
Arriba filter: 220 rows -> 32 PASS; wrote aih-tih-sc-8c7069-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-8c7069-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-8c7069-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt