Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/d12cdad7cf8422e5717c0f816993e3/659_cfy-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/123f93dbac1b62154ed1e5985c0933/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/123f93dbac1b62154ed1e5985c0933/.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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 242
  Pass (FILTER=PASS): 13 (5.4%)
  Fail (FILTER=FAIL): 229 (94.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 97
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 33
  confidence_below_min(low<high): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3

Breakdown by confidence:
  high: 13 pass, 1 fail (total: 14)
  low: 0 pass, 95 fail (total: 95)
  medium: 0 pass, 133 fail (total: 133)
Arriba filter: 242 rows -> 13 PASS; wrote 659_cfy-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_cfy-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_cfy-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt