Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/6d09cb70b20796585302330bfb6869/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/6d09cb70b20796585302330bfb6869/.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/d2/0ed95fc57d3561fcca4cccba45a3fc/659_cB6-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 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 125
  Pass (FILTER=PASS): 22 (17.6%)
  Fail (FILTER=FAIL): 103 (82.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 25
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 5
  total_reads_below_min(4.0<8.0): 3
  total_reads_below_min(3.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  total_reads_below_min(6.0<8.0): 2
  total_reads_below_min(5.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 2

Breakdown by confidence:
  high: 22 pass, 12 fail (total: 34)
  low: 0 pass, 38 fail (total: 38)
  medium: 0 pass, 53 fail (total: 53)
Arriba filter: 125 rows -> 22 PASS; wrote 659_cB6-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_cB6-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_cB6-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt