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mrbayes checkpoint file not starting from linux or windows after accidental closing
 Division 1 has 284 unique site patterns
   Initializing conditional likelihoods
   Using standard non-SSE likelihood calculator for division 1 (single-precision)
   Getting values from previous run
   Executing file "C:\Users\Public\Documents\ngfrphylogeny3\mrbayesfasta1209c.nex.ckp"
   UNIX line termination
   Longest line length = 60503
   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
      Could not find parameter 'revmat': ignoring values
      Could not find parameter 'revmat': ignoring values
      Could not find parameter 'revmat': ignoring values
      Could not find parameter 'revmat': ignoring values
      Could not find parameter 'revmat': ignoring values
      Could not find parameter 'revmat': ignoring values
      Could not find parameter 'revmat': ignoring values
      Could not find parameter 'revmat': ignoring values
      Could not find parameter 'alpha': ignoring values
      Could not find parameter 'alpha': ignoring values
      Could not find parameter 'alpha': ignoring values
      Could not find parameter 'alpha': ignoring values
      Could not find parameter 'alpha': ignoring values
      Could not find parameter 'alpha': ignoring values
      Could not find parameter 'alpha': ignoring values
      Could not find parameter 'alpha': ignoring values
      Could not find parameter 'pinvar': ignoring values
      Could not find parameter 'pinvar': ignoring values
      Could not find parameter 'pinvar': ignoring values
      Could not find parameter 'pinvar': ignoring values
      Could not find parameter 'pinvar': ignoring values
      Could not find parameter 'pinvar': ignoring values
      Could not find parameter 'pinvar': ignoring values
      Could not find parameter 'pinvar': ignoring values
      Successfully set starting values
      Could not find move 'dirichlet(revmat)'
      The error occurred when reading char. 20-20 on line 1278
         in the file 'C:\Users\Public\Documents\ngfrphylogeny3\mrbayesfasta1209c.nex.ckp'

   Returning execution to command line ...

   Error in command "Mcmc"

MrBayes >
mrbayes
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written by omaridris5315 • omaridris5315

my convergence value at 23 million run for last 10 days was at .017623 something. out of 7 million more remaining.

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written by omaridris5315 • omaridris5315

Information about this issue is posted in a different thead: How to continue a interrupted MrBayes tree analysis?

Hello Mensur, Could you look at my case too? interruption issue but a different error. This is the second time I face and I rerun it. I have a pc and it is slow as I am not yet sure how to use gpu or mpi option to start over, I have wasted 20 days between two runs.

Thankyou.

• 0 views • link
written by GenoMax GenoMax

1 answer

Never mind I figured it was mcmc setup was missing samplingfreq abd others in lset data.

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written by omaridris5315 • omaridris5315

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