Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/0f8108be961c6c386d10432f73ad4d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/0f8108be961c6c386d10432f73ad4d/.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/c8/36899d7fe3ec5d4cc84ae9c3b35b4d/659_Dl-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.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: 66
  Pass (FILTER=PASS): 3 (4.5%)
  Fail (FILTER=FAIL): 63 (95.5%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 6
  total_reads_below_min(4.0<8.0): 5
  total_reads_below_min(3.0<8.0): 4
  confidence_below_min(medium<high): 4
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 4
  total_reads_below_min(7.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 1
  total_reads_below_min(6.0<8.0): 1
  total_reads_below_min(5.0<8.0): 1
  total_reads_below_min(4.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(medium<high);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 3 pass, 14 fail (total: 17)
  low: 0 pass, 22 fail (total: 22)
  medium: 0 pass, 27 fail (total: 27)
Arriba filter: 66 rows -> 3 PASS; wrote 659_Dl-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered.tsv and 659_Dl-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_Dl-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filter_summary.txt