Difficulty with Muscle Sequence Alignment

Question

[rc16955]

Hi all,

I am trying to perform an alignment of 11 very long (whole chromosome) DNA sequences using Muscle 3.8.31 for Linux, but am encountering a problem.

This is my input:

muscle-3.8.1 -diags -in S_ratti_Chr2.fa -out S_ratti_Chr2.afa

The code seems to run for a while, but then I get the following:

    S_ratti_Chr2 11 seqs, max length 16759905, avg  length 16759518
00:48:36  1053 MB(65%)  Iter   1    1.52%  K-mer dist pass 1
00:48:47  1053 MB(65%)  Iter   1  100.00%  K-mer dist pass 1
00:48:47  1053 MB(65%)  Iter   1    1.52%  K-mer dist pass 2
00:48:47  1053 MB(65%)  Iter   1  100.00%  K-mer dist pass 2
00:49:07  24533 MB(100%)  Iter   1   10.00%  Align node       
/cm/local/apps/torque/4.2.4.1/spool/mom_priv/jobs/4974615.master.cm.cluster.SC: line 15: 95045 Killed                  muscle-3.8.1 -diags -in S_ratti_Chr2.fa -out S_ratti_Chr2_2.afa

No output file is generated. I am very new to bioinformatics and this is the first time I have attempted to use Muscle (or any aligning method); could anyone help me understand why the command is failing? Lay terminology would be greatly appreciated as I am also not very familiar with coding. I'd also like to hear of any other aligning methods if there are any generally considered better than Muscle.

Many thanks in advance.

[natasha.sernova]

See Muscle manual, it may be useful. There is no limit on sequence length,

http://www.drive5.com/muscle/muscle.html

I would suspect some atypical symbol in the sequence (different from ACGT).

Although it started running, but was killed on the first iteration...

Another alignment program, a younger one is Mafft. Below there is its web-site.

http://mafft.cbrc.jp/alignment/software/

[rc16955]

Many thanks for your reply; I am not sure that the problem is one of an atypical character as it seems to stop at different places each time I run it, for example another attempt produced the report "line 15: 103937 Killed". Nevertheless, would you be able to recommend a way of identifying atypical characters in the fasta?

And thank you for linking to Mafft; I will look into it.

[microfuge]

Are you running it locally on your computer or on a cluster ?

[GenoMax]

Looks like this is being run on a cluster.

First thing to check would be to see how much memory is being consumed. I suspect that you may be running out of it/hitting a quota.