Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/9d6bb01e4273ab072e7b8a210107de/FFPE_HD789_01_RNA_13_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/55dce3f12be93130daee0a2962f407/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/55dce3f12be93130daee0a2962f407/.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-5ae5f7b1-ce8a-4a12-9374-820c751df9c5/09/a7ecdb27117590dd6e7bf9e221420e/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 14 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 398
  Pass (FILTER=PASS): 59 (14.8%)
  Fail (FILTER=FAIL): 339 (85.2%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 14
  All 14 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 58
  confidence_below_min(medium<high): 56
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 36
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 27
  confidence_below_min(low<high): 25
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 24
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 19
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 14
  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): 12
  confidence_below_min(medium<high);total_reads_below_min(5.0<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): 7
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 5

Breakdown by confidence:
  high: 59 pass, 7 fail (total: 66)
  low: 0 pass, 171 fail (total: 171)
  medium: 0 pass, 161 fail (total: 161)
Arriba filter: 398 rows -> 59 PASS; wrote FFPE_HD789_01_RNA_13_A23WJ53LT4_1.arriba.fusions.filtered.tsv and FFPE_HD789_01_RNA_13_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_HD789_01_RNA_13_A23WJ53LT4_1.arriba.fusions.filter_summary.txt