Question: Execute command error in MrBayes
0
gravatar for rfairb
11 days ago by
rfairb0
rfairb0 wrote:

Hello,

I am working on a whole plastome phylogeny for some members of a plant family. I have aligned 12 sequences of about 160,000 bp long each. When I try to execute the .nex alignment file in MrBayes it gives me this error: Error while parsing a string. Token "TTTTGGGCGAACGACGGGAA...[followed by at least 99970 more charectors]" is too long. Maximum allowed length of a token is 99990 The error occurred when reading char. 99979-99998 on line 24 in the file 'consensus_trimmed_withoutref.nex'

But I cannot find anything about a sequence length limit in MrBayes. Does anyone have any pointers for me?

Thanks.

software error • 119 views
ADD COMMENTlink written 11 days ago by rfairb0

I guess the limit is 99990 as clearly reported by that message. See also https://github.com/NBISweden/MrBayes/issues/109 and https://github.com/NBISweden/MrBayes/issues/113

ADD REPLYlink modified 11 days ago • written 11 days ago by ATpoint19k

Thanks for your response! The links you provided were helpful. While there's no sequence length limit, there is a token limit (which is the 99990) so the links correctly suggested that an interleaved file format would work.

ADD REPLYlink written 10 days ago by rfairb0

Thanks for following up. Can you maybe post a short answer that describes what to do so we can refer users with the same question to this thread in the future?

ADD REPLYlink written 10 days ago by ATpoint19k

I was using geneious, so I just had to select the interleaved option when exporting as a nexus file.

ADD REPLYlink written 5 days ago by rfairb0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 984 users visited in the last hour