Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/dfac321646418140925daac16cc27a/aih-tih-sc-816ec7-R1_A23YTGFLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/3a178b8ee82f974610250c9db3e367/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/3a178b8ee82f974610250c9db3e367/.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 12 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 270
  Pass (FILTER=PASS): 31 (11.5%)
  Fail (FILTER=FAIL): 239 (88.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 12
  All 12 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 36
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 29
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 24
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 22
  confidence_below_min(low<high): 20
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(5.0<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(medium<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4

Breakdown by confidence:
  high: 31 pass, 5 fail (total: 36)
  low: 0 pass, 136 fail (total: 136)
  medium: 0 pass, 98 fail (total: 98)
Arriba filter: 270 rows -> 31 PASS; wrote aih-tih-sc-816ec7-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-816ec7-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-816ec7-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt