Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/28af5e82f160cdf3354648a535f366/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/28af5e82f160cdf3354648a535f366/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/3996a902a1b04b43958e01a4dcb162/V4_0001_RNA_0001_23H5VFLT4_s13.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-5b456d70-fab3-4fcc-916c-bc437f411fba/48/d36e0303d259ad82d7d96e756f6134/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 120
  Pass (FILTER=PASS): 20 (16.7%)
  Fail (FILTER=FAIL): 100 (83.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 11
  confidence_below_min(medium<high): 7
  confidence_below_min(low<high): 6
  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): 5
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  total_reads_below_min(3.0<8.0): 2
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 2
  aih_curated_blacklist: 1

Breakdown by confidence:
  high: 20 pass, 3 fail (total: 23)
  low: 0 pass, 78 fail (total: 78)
  medium: 0 pass, 19 fail (total: 19)
Arriba filter: 120 rows -> 20 PASS; wrote V4_0001_RNA_0001_23H5VFLT4_s13.arriba.fusions.filtered.tsv and V4_0001_RNA_0001_23H5VFLT4_s13.arriba.fusions.filtered_pass_only.tsv
Summary written to: V4_0001_RNA_0001_23H5VFLT4_s13.arriba.fusions.filter_summary.txt