Resource Usage
Typical resource requirements for CheckRef processes.
Process Resources
| Process | CPUs | Memory | Time (typical) |
|---|---|---|---|
| VALIDATE_VCF_FILES | 1 | 4 GB | 5 min |
| CHECK_ALLELE_SWITCH | 1 | 4-8 GB | 30 min - 2 h |
| REMOVE_SWITCHED_SITES | 1 | 4 GB | 10-30 min |
| CORRECT_SWITCHED_SITES | 1 | 4 GB | 10-30 min |
| VERIFY_CORRECTIONS | 1 | 4 GB | 30 min - 2 h |
| CREATE_SUMMARY | 1 | 2 GB | 5 min |
Factors Affecting Runtime
- VCF size: Larger files take longer
- Number of variants: More variants = more comparisons
- Reference panel size: Larger panels = more memory
- Chromosome: chr1 (largest) takes longest
Optimization Tips
- Run whole genome in parallel (all chromosomes at once)
- Use local fast storage for work directory
- Increase CPUs for CHECK_ALLELE_SWITCH to 2-4
- Use SSD storage for better I/O
- Enable
-resumefor failed runs
Resource Planning
Small dataset (1 chromosome):
- Total time: 1-2 hours
- Peak memory: 8 GB
- Storage: 10 GB
Whole genome (22 autosomes):
- Total time: 4-8 hours (parallel)
- Peak memory: 8 GB per chromosome
- Storage: 100-500 GB
See Also
- Configuration - Resource customization
- Running - Execution best practices