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Question: MrBayes Log likelihood stuck on a single value
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Entering edit mode

Hi All,
I think the below phenomenon may be (in part) a Beagle library issue, but there may be more going on?
I am trying to run a MrBayes analysis on protein alignment (3 partitions). I think there might be a bug.
When I run the analysis locally (no Beagle), everything looks ok, however, when I run the analysis on a cluster (either at the U or on cipres) I get a LnL of -inf. It doesn’t matter how long I run. In addition, the other parameters are stuck at the initial estimate. I think that this is, at least in part, due to use of Beagle. When I turn of Beagle, I now get some of the estimates to change, but the LnL still gets stuck at a ridiculous value (-1.797693e+308; see attached parameter file).

The first couple of lines of parameter file run at cipres (no Beagle) look like this (note that LnL is not changing)

Gen LnL LnPr    TL{all} alpha{1}    alpha{2}    alpha{3}    pinvar{1}   
0           -1.797693e+308  1.557647e+02    4.740000e+00    1.000000e+00    1.000000e+00    
1000    -1.797693e+308  1.561742e+02    4.740000e+00    5.905880e-01    1.000000e+00    
2000    -1.797693e+308  1.551478e+02    4.740000e+00    1.616992e+00    1.000000e+00    
3000    -1.797693e+308  1.561978e+02    4.740000e+00    5.669044e-01    1.000000e+00    
4000    -1.797693e+308  1.564849e+02    4.740000e+00    2.798501e-01    1.000000e+00    
5000    -1.797693e+308  1.567126e+02    4.740000e+00    5.213185e-02    1.000000e+00
6000    -1.797693e+308  1.562584e+02    4.740000e+00    5.063503e-01    1.000000e+00

When I run it locally (notice that at least the LnL is changing)

Gen LnL LnPr    TL{all} alpha{1}    alpha{2}    alpha{3}    pinvar{1}   
0         -1.797693e+308    1.557647e+02    4.740000e+00    1.000000e+00    1.000000e+00
1000    -1.652381e+05   1.565472e+02    4.740000e+00    2.175323e-01    1.000000e+00    
2000    -1.634193e+05   1.566048e+02    4.740000e+00    1.599154e-01    1.000000e+00    
3000    -1.623047e+05   1.566130e+02    4.740000e+00    1.517907e-01    1.000000e+00

Below is the MrBayes block from the Nexus file

begin mrbayes;  
    set autoclose=yes;

    charset Subset1 = 1-979;
    charset Subset2 = 980-2133;
    charset Subset3 = 2134-2838;

    partition PartitionFinder = 3:Subset1, Subset2, Subset3;
    set partition=PartitionFinder;

    unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all) tratio=(all);

    lset applyto=(1) rates=invgamma;
    prset applyto=(1) aamodelpr=mixed ratepr=variable;
    lset applyto=(2) rates=invgamma;
    prset applyto=(2) aamodelpr=mixed ratepr=variable;
    lset applyto=(3) rates=invgamma;
    prset applyto=(3) aamodelpr=mixed ratepr=variable;

    mcmcp ngen=50000000 savebrlens=yes samplefreq=1000 printfreq= 1000;
    propset ExtTBR$prob=0;
    mcmc;
end;

I would appreciate any insights! Thanks

ADD COMMENTlink 3.1 years ago Whetting ♦ 1.5k • updated 15 months ago uzmaabdulsalam • 0
Entering edit mode
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Hi All, I'm also running Bayesian analysis using MrBayes in CIPRES on concatenated alignment with three partitions but when I ran it the run doesn't show three partitions, beside this it ran fine.... I double check many times but I'm not sure where I did mistake in using parameters. can anyone help me out in this?

The run appeared like this which showed no partitions:

Successfully read matrix
      Setting default partition (does not divide up characters)
      Setting model defaults
      Seed (for generating default start values) = 1542224193
      Setting output file names to "infile.nex.run<i>.<p|t>"
   Exiting data block
   Reached end of file

MrBayes > 
   Setting outgroup to taxon "Trichophorum_alpinum"

MrBayes > 
   Successfully set likelihood model parameters

MrBayes > 
   Setting Nst to 6
   Successfully set likelihood model parameters

MrBayes > 
   Setting Nucmodel to 4by4
   Set state frequency prior to default
   Successfully set likelihood model parameters

MrBayes > 
   Setting Rates to Invgamma
   Successfully set likelihood model parameters

MrBayes > 
   Successfully set likelihood model parameters

MrBayes > 
   Setting Pinvarpr to Uniform(0.00,1.00)
   Successfully set prior model parameters

MrBayes > 
   Setting Aamodelpr to Fixed(Gtr)
   Successfully set prior model parameters

MrBayes > 
   Setting Ratepr to Variable [Dirichlet(..,1,..)]
   Successfully set prior model parameters

MrBayes > 
   Setting Statefreqpr to Dirichlet(0.25,0.25,0.25,0.25)
   Successfully set prior model parameters

MrBayes > 
   Setting Revmatpr to Dirichlet(1.00,1.00,1.00,1.00,1.00,1.00)
   Successfully set prior model parameters

MrBayes > 
   Setting Ratecorrpr to Uniform(-1.00,1.00)
   Successfully set prior model parameters

MrBayes > 
   Setting Covswitchpr to Uniform(0.00,100.00)
   Successfully set prior model parameters

MrBayes > 
   Setting Tratiopr to Beta(1.00,1.00)
   Successfully set prior model parameters

MrBayes > 
   Setting Brlenspr to Unconstrained:Exponential(10.00)
   Successfully set prior model parameters

MrBayes > 
   Expecting '; or <number>'
   Instead found '1560charset' in command 'Databreaks' at position 18

MrBayes > 
   Defining charset called 'ETS'

MrBayes > 
   Defining charset called 'ITS'

MrBayes > 
   Not reporting site rates

MrBayes > 
   Setting reversible rate matrix (revmat) format to Dirichlet

MrBayes > 
   Setting number of generations to 10000000
   Setting number of runs to 2
   Setting number of chains to 4
   Setting heating parameter to 0.200000

Thank you! Best,

ADD REPLYlink 15 months ago
uzmaabdulsalam
• 0
• updated 15 months ago
genomax
68k

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