clustalo - align milions of short seq, memory issue

Question

[emmanouil.a]

Hi, I'm looking to run clustalo with some milions of short sequences but it gives me the below error:

**Couldn't allocate MPI memory (symmatrix.c|NewSymMatrix) FATAL: Memory
allocation for distance matrix failed**

Is it a memory limitation related to the tool/code or the PC I'm using to run the tool? In clustalo help I can not find any option to increase the memory.

Any idea how to solve it? Thanks a lot!

[GenoMax]

I'm looking to run clustalo with some milions of short sequences

What is the use case for this? There is likely going to be better option than simply trying do a MSA of millions of reads.

Answer 1

[Mensur Dlakic]

Is it a memory limitation related to the tool/code or the PC I'm using to run the tool?

It is. That's what the error message is telling you.

Two ways of solving it: 1) get a computer with more memory; 2) maybe define your problem better so you don't have to align millions of sequences, as no multiple alignment tool is designed for that kind of sequence number. Not even sure what anyone would do with an alignment of millions of sequences, and chances are that you can define the problem on a smaller scale where the outcome would still be informative.

[emmanouil.a]

Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.