append=yes returning error in mcmc line

[linley-sherin]

Hello! I am having repeated issues with trying to append a disrupted analysis. It is a large analysis which ran for a week on a cluster and then hit the cluster time limit before it finished - so I need to start it again from where it ended. I have also replicated this issue on mrbayes 3.2.7 locally which I am running on Ubuntu from the command line. The analysis is being run within the same directory with the .nex, .ckp, .t and .p files.

The infile.nex is the exact same as when I started it from scratch except that I added append = yes, see here:

mcmc ngen=100000000 nruns=2 printfreq=10000 samplefreq=10000 nchains=4 diagnfreq=10000 stoprule=yes stopval=0.005 savebrlens=yes append=yes;
sump relburnin=yes burninfrac=0.25;
sumt relburnin=yes burninfrac=0.25 contype=halfcompat conformat=simple;

This is the current error message:

Error appending to previous run
      Error in command "Mcmc"
      There was an error on at least one processor
      The error occurred when reading char. 69443318-69443317 on line 661
         in the file 'infile.nex'

Where there is not a character 69443318. I have tried deleting and rewriting the line - as well as only copying and pasting the text I want just in case there is a stray character somewhere.

Other things I have tried:

• Copying the .ckp file into the infile.nex file as I saw that recommended also. I got an error that I needed to add a full trees block with extra parameters which I do not want to do (and doesn't seem necessary based on what the manual prescribes).
• Starting a new analysis locally, cancelling it and trying to append (just to ensure it's not the cluster ruining my files). I get the same error.
• Adding the following arguments to the mcmc line because I saw this also recommended (though I am pretty sure these are just restating the defaults?):
  checkpoint=yes startparams=current starttree=current
• Checking that all generation counts match between files - they do.

Would you be able to compile and run MrBayes to test fixes to this bug?

• Yes, I know how to use git and how to compile MrBayes.
• No, sorry.

What is the environment that you run MrBayes in?

• Operating system (including variant and release):
• Version of MrBayes: MrBayes 3.2.7a x86_64
• If possible, include the output of the Version command in MrBayes below:

MrBayes, Bayesian Analysis of Phylogeny

Version:   3.2.7a
Features:  SSE AVX Beagle MPI
Host type: x86_64-unknown-linux-gnu (CPU: x86_64)
Compiler:  gnu 11.2.0