Unicycler error not enough memory available

Question

[A_heath]

Hi all,

I have large paired-end fastq files (13 GB each) obtained from Illumina sequencing of a bacterial genome.

I am running Unicycler to assemble these WGS data. However, when it uses spades-hammer, I got the following error message:

The reads contain too many k-mers to fit into available memory. You need approx. 13.0774GB of free RAM to assemble your dataset

By any chance, is there a way to solve this issue?

Thank you so much for your help!

Audrey

[Joe]

You need more RAM. How much does the computer you are running this on have?

There's no way to solve this beyond running it on a higher-powered computer, or downsampling your data but we'd need to know more about the way it was sequenced to know if you can do the latter without issue. Looking at some of our past microbial NGS, 13GB would be at the high end, so you perhaps could downsample and still have enough coverage (but you're better off just getting access to a better machine).

[Mensur Dlakic]

In my experience, megahit has lower memory requirements than Spades, but don't know about Unicycler.