Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/77d016916893cfbe1f9a4a553a8d62/659_ecd-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/a4163cb3cbb087765b82b535be2421/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/a4163cb3cbb087765b82b535be2421/.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 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 324
  Pass (FILTER=PASS): 46 (14.2%)
  Fail (FILTER=FAIL): 278 (85.8%)

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

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 30
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 30
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 30
  confidence_below_min(medium<high): 29
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 25
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 24
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 19
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(low<high): 11
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  total_reads_below_min(3.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5

Breakdown by confidence:
  high: 46 pass, 18 fail (total: 64)
  low: 0 pass, 131 fail (total: 131)
  medium: 0 pass, 129 fail (total: 129)
Arriba filter: 324 rows -> 46 PASS; wrote 659_ecd-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered.tsv and 659_ecd-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_ecd-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filter_summary.txt