Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/fb7de28d82a0ba93f40400f2762cc3/659_cfy-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/1aaaac0bd07a0882a2314e39fd6980/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/1aaaac0bd07a0882a2314e39fd6980/.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-6a8e5f46-8592-47ae-b09e-a1efe7f02cb2/6a/80a8f8c27f6b00a3a33e35ea914965/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: 126
  Pass (FILTER=PASS): 5 (4.0%)
  Fail (FILTER=FAIL): 121 (96.0%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 23
  confidence_below_min(medium<high): 20
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(low<high): 2

Breakdown by confidence:
  high: 5 pass, 3 fail (total: 8)
  low: 0 pass, 31 fail (total: 31)
  medium: 0 pass, 87 fail (total: 87)
Arriba filter: 126 rows -> 5 PASS; wrote 659_cfy-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered.tsv and 659_cfy-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filter_summary.txt