Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/d119ae9734ce94f8d112016732eff1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/d119ae9734ce94f8d112016732eff1/.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/e4/8d416bd0e783fee938c28f5891bd2c/659_ri-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.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 3 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 123
  Pass (FILTER=PASS): 7 (5.7%)
  Fail (FILTER=FAIL): 116 (94.3%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 23
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 19
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(7.0<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(0.0<8.0): 6
  confidence_below_min(low<high): 5
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(3.0<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(4.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  total_reads_below_min(6.0<8.0): 1
  total_reads_below_min(5.0<8.0): 1

Breakdown by confidence:
  high: 7 pass, 3 fail (total: 10)
  low: 0 pass, 50 fail (total: 50)
  medium: 0 pass, 63 fail (total: 63)
Arriba filter: 123 rows -> 7 PASS; wrote 659_ri-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_ri-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_ri-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt