Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/0475dea135b5633b403846d79a1e2d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/0475dea135b5633b403846d79a1e2d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/6dbdc5e6e2ea6dde5cc92f0e8c2d2f/FFPE_V4_0001_RNA_0003_B23MHV2LT4_2.arriba.fusions.tsv
  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-40cc52c0-5bec-40b6-b04d-c64c51f55eff/cf/a844d18c3db3aeda7471fb3d005c4f/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 149
  Pass (FILTER=PASS): 20 (13.4%)
  Fail (FILTER=FAIL): 129 (86.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 27
  confidence_below_min(low<high): 22
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(medium<high): 8
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2
  aih_curated_blacklist: 1

Breakdown by confidence:
  high: 20 pass, 3 fail (total: 23)
  low: 0 pass, 93 fail (total: 93)
  medium: 0 pass, 33 fail (total: 33)
Arriba filter: 149 rows -> 20 PASS; wrote FFPE_V4_0001_RNA_0003_B23MHV2LT4_2.arriba.fusions.filtered.tsv and FFPE_V4_0001_RNA_0003_B23MHV2LT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_V4_0001_RNA_0003_B23MHV2LT4_2.arriba.fusions.filter_summary.txt