Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/4760837fe61bc32cc33ab74041a5a0/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/b6da5f9d12ab5d38b7a4f201ac9f92/659_bGc-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/4760837fe61bc32cc33ab74041a5a0/.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 2 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 88
  Pass (FILTER=PASS): 1 (1.1%)
  Fail (FILTER=FAIL): 87 (98.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 2
  All 2 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 17
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 3
  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);aih_curated_blacklist: 2
  confidence_below_min(low<high): 2
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 1

Breakdown by confidence:
  high: 1 pass, 2 fail (total: 3)
  low: 0 pass, 25 fail (total: 25)
  medium: 0 pass, 60 fail (total: 60)
Arriba filter: 88 rows -> 1 PASS; wrote 659_bGc-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered.tsv and 659_bGc-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filter_summary.txt