memory allocation problem

[furqan915]

Hi,
I have used rhierbaps previously on 27 genomes' core alignment and it worked fine. But now I am working on 557 genomes's core alignment (file size = 1.6 gb). I have used this command and following message shows up:

> snp.matrix <- load_fasta("./clean.full.aln")
Error: cannot allocate vector of size 11.7 Gb

Is it issue with my system or the package?
My Linux PC has 4 cores and 8gb.
Thanks

[gtonkinhill]

Hi,

rhierbaps is not particularly efficient so it looks like you have run out of memory on your system.
I would recommend having a look at fastbaps. This was designed to work with larger datasets and should speed things up quite a bit.

You could also consider using snp-sites to reduce the alignment to just variable columns before passing the reduced alignment to either rhierbaps or fastbaps