Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/9d86f7df0ee971b71de555b4f1f388/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/9d86f7df0ee971b71de555b4f1f388/.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/cd/18b917bf978ce7c7802f276c362100/659_bTq-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 12 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 322
  Pass (FILTER=PASS): 36 (11.2%)
  Fail (FILTER=FAIL): 286 (88.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 12
  All 12 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 93
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 35
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 16
  confidence_below_min(low<high): 16
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 5
  total_reads_below_min(5.0<8.0): 2

Breakdown by confidence:
  high: 36 pass, 8 fail (total: 44)
  low: 0 pass, 134 fail (total: 134)
  medium: 0 pass, 144 fail (total: 144)
Arriba filter: 322 rows -> 36 PASS; wrote 659_bTq-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_bTq-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt