Muscle alignment error

Question

[hypeanut]

Hi, I wanted to align several genomes, and I used the cat command to form a fasta file containing all DNA sequences of several organisms. Then I tried to use Muscle to perform the alignment in the terminal by typing in:

$muscle -in input.fasta -fastaout output.afa

However, the program ended itself and reported:

try 3999 seqs, lengths min 501, max 9616375, avg 82643

00:51:46  1945 MB(-194%)  Iter   1  100.00%  K-mer dist pass 1

00:51:46  1945 MB(-194%)  Iter   1  100.00%  K-mer dist pass 2

Killed29  8544 MB(-851%)  Iter   1    2.40%  Align node

Could someone please help me interpreting this error message? Thanks in advance!

[GenoMax]

What kind of "genomes" are these? Considering min and max values of size that seems like a rather wide range for these to be comparable using a multiple sequence alignment.

Answer 1

[Mensur Dlakic]

It looks like you have ~330 million residues. Muscle is not meant for aligning that kind of data - most aligners aren't either. The program likely gets killed because it blows through the available memory. Even if it didn't, it would take longer than what you could wait for.