MrBayes Restart

[uzm...@fjwu.edu.pk]

Hello All,

I have run Bayesian analysis using MrBayes for 20 million generations. One cycle of 20 million generations were completed and started another but then in the middle the run reached the time limit. I carefully read MrBayes Restart option and then ran the analysis again but every time  I got the following error, can anyone please help me out why this is so:

Division 1 has 720 unique site patterns
      Division 2 has 590 unique site patterns
      Division 3 has 319 unique site patterns
      Initializing conditional likelihoods
      Using standard SSE likelihood calculator for division 1 (single-precision)
      Using standard SSE likelihood calculator for division 2 (single-precision)
      Using standard SSE likelihood calculator for division 3 (single-precision)
      Initializing invariable-site conditional likelihoods
      Getting values from previous run

      Executing file "infile.nex.ckp"...

   UNIX line termination
   Longest line length = 48343
   Parsing file
   Expecting NEXUS formatted file
   Reading trees block
      Successfully read tree 'mcmc.tree_1'
      Successfully read tree 'mcmc.tree_2'
      Successfully read tree 'mcmc.tree_3'
      Successfully read tree 'mcmc.tree_4'
      Successfully read tree 'mcmc.tree_5'
      Successfully read tree 'mcmc.tree_6'
      Successfully read tree 'mcmc.tree_7'
      Successfully read tree 'mcmc.tree_8'
   Exiting trees block
   Reading mrbayes block
      The parameter 'Ratemultiplier{all}' is fixed so the starting value cannot be set
      There was an error on at least one processor
      The error occurred when reading char. 27 on line 1037
         in the file 'infile.nex.ckp'

   Returning execution to calling file ...

      Error in command "Mcmc"
      There was an error on at least one processor
      The error occurred when reading char. 27 on line 989
         in the file 'infile.nex'
   Error in command "Execute"

MrBayes >    End of File encountered on stdin; quitting

   Deleting previously defined characters
   Deleting user trees
   Deleting previously defined taxa
   Quitting program

Best,

Uzma

[Mark Miller]

Hi Uzma,

Sorry for my slow response.

I cant tell for certain on this with the information you provided. It seems to me that the most likely error is this:

The parameter 'Ratemultiplier{all}' is fixed so the starting value cannot be set

But if that is the error, I cant tell why you were able to start the run in the first place, unless you accidentally swapped the input files.
If you have not got it re-started already, I would look at the initial run, and see if the string  
Ratemultiplier{all} is in the original input file, and if it produced this same error message in the stdout.txt file. In other words, is this error fatal or non-fatal.
If you find this message in output of the first run, it is non-fatal and we must look elsewhere. 

If you see it is non-fatal, please send me the file _jobinfo.txt, and I can take a look.
Best,
Mark