Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/32672eafe693c34991b46749dc4b6f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/32672eafe693c34991b46749dc4b6f/.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/fa/ab8c1796407590e9156d6accd97f28/659_dRe-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 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 305
  Pass (FILTER=PASS): 32 (10.5%)
  Fail (FILTER=FAIL): 273 (89.5%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 100
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 40
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 24
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 16
  confidence_below_min(low<high): 11
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3

Breakdown by confidence:
  high: 32 pass, 5 fail (total: 37)
  low: 0 pass, 126 fail (total: 126)
  medium: 0 pass, 142 fail (total: 142)
Arriba filter: 305 rows -> 32 PASS; wrote 659_dRe-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_dRe-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_dRe-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt