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liaoherui / StrainScan

High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers
https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01615-w
MIT License
32 stars 4 forks source link

Build custom database use too much memory #12

Closed wsyjh closed 9 months ago

wsyjh commented 9 months ago

Hello！Thank you for the tools you developed. When I build a custom database, It will need about twice as much memory as the number of strains. Is there any way to reduce the amount of memory?

liaoherui commented 9 months ago

Hi, thanks for using StrainScan!

As mentioned in our manuscript, the memory and time usage during database construction is still a limitation of our tool when there are a super large number of input strain genomes. However, you may consider using -e 1 to reduce the memory usage. Nevertheless, if your input contains a super large number of strains (e.g. more than 5000 strains), then it could still be a problem.