Calculation killed when running conservation calcultions on large fasta files

[JC]

Hello,

when I run the code below for large fasta files (from 200 MB to 2 GB), the job is soon killed without giving any informative error message. However, when I run the same script on smaller fasta files, it runs without problems, so I guess it's a memory allocation issue.

aln <- read.fasta(file = i, to.upper = TRUE) 
similarity <- conserv(x=aln$ali, method="similarity", sub.matrix="bio3d", normalize.matrix = TRUE)

Any idea on how to sort this out?

Thank you

Regards

Juan