Execute command error in MrBayes

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4.8 years ago

rfairb ▴ 10

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 • 3.2k views

ADD COMMENT • link updated 3.8 years ago by Biostar 20 • written 4.8 years ago by rfairb ▴ 10

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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 REPLY • link 4.8 years ago by ATpoint 82k

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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 REPLY • link 4.8 years ago by rfairb ▴ 10

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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 REPLY • link 4.8 years ago by ATpoint 82k

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

ADD REPLY • link 4.8 years ago by rfairb ▴ 10

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