Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/7364adcb0d86c62688777b98511a0b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/7364adcb0d86c62688777b98511a0b/.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/93/1a6fab5e5c56c1efc7a9109d800d2d/tih_rna_sample_00588_B23MVV7LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-7324c8a8-f474-426a-a5c9-715912777f94/d8/92d6652b0b8fcc763d0f3fff270437/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: 223
  Pass (FILTER=PASS): 17 (7.6%)
  Fail (FILTER=FAIL): 206 (92.4%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 83
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 23
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 19
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(low<high): 8
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  total_reads_below_min(5.0<8.0): 2

Breakdown by confidence:
  high: 17 pass, 8 fail (total: 25)
  low: 0 pass, 74 fail (total: 74)
  medium: 0 pass, 124 fail (total: 124)
Arriba filter: 223 rows -> 17 PASS; wrote tih_rna_sample_00588_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00588_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00588_B23MVV7LT4_1.arriba.fusions.filter_summary.txt