Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/7d7c2cd777db2e65968a286443a8e8/659_On-T1-TRNA-2_B23MHV2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/1700d72f96f26d422edce382536ad7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/1700d72f96f26d422edce382536ad7/.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: 267
  Pass (FILTER=PASS): 19 (7.1%)
  Fail (FILTER=FAIL): 248 (92.9%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 95
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 30
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 14
  confidence_below_min(low<high): 14
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(7.0<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(2.0<8.0): 3

Breakdown by confidence:
  high: 19 pass, 2 fail (total: 21)
  low: 0 pass, 114 fail (total: 114)
  medium: 0 pass, 132 fail (total: 132)
Arriba filter: 267 rows -> 19 PASS; wrote 659_On-T1-TRNA-2_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_On-T1-TRNA-2_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_On-T1-TRNA-2_B23MHV2LT4_1.arriba.fusions.filter_summary.txt