Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/698c533e8e07626bcf5a3ed2def408/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/698c533e8e07626bcf5a3ed2def408/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/ae4e4b4d5260fc0d5f717254f296e9/GM24385_0001_RNA_0001_23H5VFLT4_s40.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 3 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 35
  Pass (FILTER=PASS): 1 (2.9%)
  Fail (FILTER=FAIL): 34 (97.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 3
  All 3 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(medium<high): 3
  confidence_below_min(low<high): 3
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 2
  total_reads_below_min(4.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(medium<high);aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 1

Breakdown by confidence:
  high: 1 pass, 1 fail (total: 2)
  low: 0 pass, 25 fail (total: 25)
  medium: 0 pass, 8 fail (total: 8)
Arriba filter: 35 rows -> 1 PASS; wrote GM24385_0001_RNA_0001_23H5VFLT4_s40.arriba.fusions.filtered.tsv and GM24385_0001_RNA_0001_23H5VFLT4_s40.arriba.fusions.filtered_pass_only.tsv
Summary written to: GM24385_0001_RNA_0001_23H5VFLT4_s40.arriba.fusions.filter_summary.txt