Entering edit mode
3.6 years ago
taylor • 0
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
Centrifuge also can be useful https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5131823/
Are you sure bowtie is the right tool for the job? Which index are you building?
They are some environment microbes... I think bowtie is easy to use. Do you have some software recommended for this job? Thanks,
Those microbes may have highly similar sequences, making alignment erroneous. Take a look at kraken2 for species classification
OK. Thanks. I will try.
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 ?