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How to index a large fasta file (>100GB) by using bowtie2-build

I am wondering how to index a very large fasta file (~100GB) by using bowtie2-build? I have enlarged my memory up to 512G and use the parameter "--bmax 3 --dcv 4096" to minimize the memory usage, but it still failed...

So is there any possible solution to solve this problem? Thanks~

Here is the error message:

Using parameters --bmax 3 --dcv 4096

Doing ahead-of-time memory usage test

Ran out of memory; automatically trying more memory-economical parameters.

Total time for call to driver() for forward index: 01:17:56

Thanks,

alignment genome bowtie index
• 3,661 views • link
updated by WouterDeCoster WouterDeCoster • written by taylor • taylor

Are you sure bowtie is the right tool for the job? Which index are you building?

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written by WouterDeCoster WouterDeCoster

They are some environment microbes... I think bowtie is easy to use. Do you have some software recommended for this job? Thanks,

• 0 views • link
written by taylor • taylor

Those microbes may have highly similar sequences, making alignment erroneous. Take a look at kraken2 for species classification

• 0 views • link
written by WouterDeCoster WouterDeCoster

OK. Thanks. I will try.

• 0 views • link
written by taylor • taylor

Maybe you could try bwa mem ? what do you want to do with the index ? which type of data ? which type of organism are you studying ?

• 0 views • link
written by Nicolas Rosewick Nicolas Rosewick

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