Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/02002029f8ea4203c9344d65b718d4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/4ae09b077293b8904c6d4d355eeb20/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/02002029f8ea4203c9344d65b718d4/.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-40cc52c0-5bec-40b6-b04d-c64c51f55eff/cf/a844d18c3db3aeda7471fb3d005c4f/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 273
  Pass (FILTER=PASS): 45 (16.5%)
  Fail (FILTER=FAIL): 228 (83.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 83
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 23
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 20
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 2

Breakdown by confidence:
  high: 45 pass, 2 fail (total: 47)
  low: 0 pass, 102 fail (total: 102)
  medium: 0 pass, 124 fail (total: 124)
Arriba filter: 273 rows -> 45 PASS; wrote 659_ciJ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_ciJ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_ciJ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt