Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/7bf5eac2a02a8117472a862c41daec/V4_0001_RNA_0005_23H5VFLT4_s43.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/7d5a85ddc9ac59178cfd7e26e65e57/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/7d5a85ddc9ac59178cfd7e26e65e57/.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-5b456d70-fab3-4fcc-916c-bc437f411fba/48/d36e0303d259ad82d7d96e756f6134/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: 82
  Pass (FILTER=PASS): 14 (17.1%)
  Fail (FILTER=FAIL): 68 (82.9%)

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(3.0<8.0): 20
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(medium<high): 7
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high): 2
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 2
  total_reads_below_min(4.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 1

Breakdown by confidence:
  high: 14 pass, 1 fail (total: 15)
  low: 0 pass, 54 fail (total: 54)
  medium: 0 pass, 13 fail (total: 13)
Arriba filter: 82 rows -> 14 PASS; wrote V4_0001_RNA_0005_23H5VFLT4_s43.arriba.fusions.filtered.tsv and V4_0001_RNA_0005_23H5VFLT4_s43.arriba.fusions.filtered_pass_only.tsv
Summary written to: V4_0001_RNA_0005_23H5VFLT4_s43.arriba.fusions.filter_summary.txt