Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/53becb72075753b49cd0d068f9f1df/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/53becb72075753b49cd0d068f9f1df/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/836b174f223a105e27a902db4278df/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.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-e543dae6-5fea-4720-bfb6-150bf1ff20d4/33/a04540cea7c8abc13163bc03b147d5/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 14 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 320
  Pass (FILTER=PASS): 42 (13.1%)
  Fail (FILTER=FAIL): 278 (86.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 14
  All 14 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 68
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 25
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 24
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 21
  confidence_below_min(low<high): 18
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5

Breakdown by confidence:
  high: 42 pass, 4 fail (total: 46)
  low: 0 pass, 118 fail (total: 118)
  medium: 0 pass, 156 fail (total: 156)
Arriba filter: 320 rows -> 42 PASS; wrote aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt