Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/81aa7b5559bbc9986ae75801a3540a/V4_0001_RNA_0005_23H5VFLT4_s30.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/0f4efd8b069e2312a2961615510b45/.command.sh
  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/5e/0f4efd8b069e2312a2961615510b45/.command.run
  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: 66
  Pass (FILTER=PASS): 9 (13.6%)
  Fail (FILTER=FAIL): 57 (86.4%)

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): 11
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(medium<high): 6
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 4
  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(medium<high);total_reads_below_min(3.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 2
  total_reads_below_min(4.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 2
  aih_curated_blacklist: 1
  total_reads_below_min(6.0<8.0): 1
  total_reads_below_min(4.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 9 pass, 5 fail (total: 14)
  low: 0 pass, 37 fail (total: 37)
  medium: 0 pass, 15 fail (total: 15)
Arriba filter: 66 rows -> 9 PASS; wrote V4_0001_RNA_0005_23H5VFLT4_s30.arriba.fusions.filtered.tsv and V4_0001_RNA_0005_23H5VFLT4_s30.arriba.fusions.filtered_pass_only.tsv
Summary written to: V4_0001_RNA_0005_23H5VFLT4_s30.arriba.fusions.filter_summary.txt