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question 1

I wanted to use sumt command after completion of mcmc run. Whenever I use, sumt Filename=infile.nex, it gives me the error:

A matrix must be specified before sumt can be used
Error when setting parameter "Filename" (1)

But for the same analysis, I can use sump without any problem. What should I do now?

question 2

Another issue, I used burn in as 25% where as in Tracer, it is always showing 10%. No matter how much burn in I use, Tracer always shows 10% as burn in.

system stats

Operating system : Centos7
Version of MrBayes: 3.2.6

Thanks in advance, Best Regards, Zillur

Harry Richman
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zillur rahman
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  • Hello zillur rahman,

    you've crossposted this question also on biostars. You should mention this, so that everyone can see, if there is already an answers to your problem.

    Thanks.

    fin swimmer

     – finswimmer Dec 13 '18 at 08:00

3 Answers3

2

Having thought this through, I think you've made a mistake. The file it wants is the outfile, you have given it the infile only. My original answer is below.

====================

From memory (my personal memory, not RAM, SSD or Stata), in the run command, you need to specify,

nruns=2

sumt will then combine both runs. If the file name is mystuff.run and nruns=2, there will be an output of mystuff.run1.t and mystuff.run2.t.

If nruns isn't set then sumt will not work, or if the MCMCMC output ends up with different names again sumt will not work.

With the burnin, you simply specify this in MrBayes. It is easy to write a script that will perform a 25% burnin. Tracer is nicely written, presumably C, its fast, but it has been around for a long time.

M__
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This is a bit late. However, I am hoping someone else will find this useful since I had the same problem.

The data matrix is your infile.nex file (the nex file you supplied for the analysis)

  1. Bracket out the mcmc command in your infile.nex
    • Prevents the file from being run again.
    • May not be present.
  2. In Mr. Bayes: Execute infile.nex
    • Loads you infile as the data matrix
  3. In Mr. Bayes: sumt Filename=infile.nex nruns=2
    • If you have nruns set in you Mr. Bayes block you can skip this.
Jeremy Buttler
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This question was posted and answered as a Github Issue in the MrBayes repository; I am copying the answer here for better visibility.

Dear zillurbmb51,

Thank you for your question. You need to load the data matrix in memory before issuing the sumt command, or in other words: "A matrix must be specified before sumt can be used".

Example 1 (where you haven't yet run a MCMC):

Start mb, then type:

exe infile.nex
mcmc
sumt

Example 2 (where you already did a MCMC, and have .t files in your current working directory, and they are named infile.nex.run1.t, infile.nex.run2.t, etc):

Start mb, then type:

exe infile.nex 
sumt filename=infile.nex

Cheers

Johan

Harry Richman
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