Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/35837c8f43328b6127fde50031e485/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/35837c8f43328b6127fde50031e485/.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/a6/7948a7fa6648a59de4d1bca6715337/659_cTi-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 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 265
  Pass (FILTER=PASS): 61 (23.0%)
  Fail (FILTER=FAIL): 204 (77.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 70
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 33
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 16
  confidence_below_min(low<high): 15
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 6
  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): 3
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2
  total_reads_below_min(7.0<8.0): 2

Breakdown by confidence:
  high: 61 pass, 6 fail (total: 67)
  low: 0 pass, 108 fail (total: 108)
  medium: 0 pass, 90 fail (total: 90)
Arriba filter: 265 rows -> 61 PASS; wrote 659_cTi-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_cTi-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_cTi-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt