Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/e49739d84108db69beffc4dae028d6/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/e49739d84108db69beffc4dae028d6/.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/ec/2cef18d68d59f79c28c5f4aabe3879/Hs746T_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-f79a17a0-988d-46c3-a0fc-cc7f26b06d9c/2f/783d5e3fc4bb0e4fc378bb3e8b5e61/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 451
  Pass (FILTER=PASS): 66 (14.6%)
  Fail (FILTER=FAIL): 385 (85.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 81
  confidence_below_min(medium<high): 74
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 36
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 32
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 28
  confidence_below_min(low<high): 21
  confidence_below_min(low<high);total_reads_below_min(4.0<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(5.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 7

Breakdown by confidence:
  high: 66 pass, 11 fail (total: 77)
  low: 0 pass, 222 fail (total: 222)
  medium: 0 pass, 152 fail (total: 152)
Arriba filter: 451 rows -> 66 PASS; wrote Hs746T_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.filtered.tsv and Hs746T_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: Hs746T_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.filter_summary.txt