Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/07175d1ba88340a1f59c6353487130/659_c95-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/31d27cb20ce0af13ab6a47055cd1ee/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/31d27cb20ce0af13ab6a47055cd1ee/.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 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 413
  Pass (FILTER=PASS): 72 (17.4%)
  Fail (FILTER=FAIL): 341 (82.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 110
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 61
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 36
  confidence_below_min(low<high): 22
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4

Breakdown by confidence:
  high: 72 pass, 4 fail (total: 76)
  low: 0 pass, 175 fail (total: 175)
  medium: 0 pass, 162 fail (total: 162)
Arriba filter: 413 rows -> 72 PASS; wrote 659_c95-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_c95-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_c95-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt