MrBayes Restart

MrBayes 3.2.2 on XSEDE Restart Interface (BETA release)

MrBayes 3.2.2 supports checkpointing, which makes it possible to restart a run that has terminated unexpectedly, or that has reached the end of the maximum allowed run time without converging. The MrBayes 3.2.2 on XSEDE Restart Interface makes it possible for users to take advantage of this feature. The current interface is admittedly fragile, but it does make it possible to access the restart capability. We plan to improve the functionality of the interface if users request a better interface.

To use the restart capability, please us the following steps exactly (note the information about failure cases at the bottom of the page):

  1. Open the results pane for a MrBayes job that you wish to restart. Confirm that the results list includes a checkpoint (.ckp) file (it is possible for a job to terminate so early this file is not created, and it is also possible to turn checkpointing off via the MrBayes block. Please see the MrBayes 3.2.2 manual for more details.)
     
  2. Identify all of the files that will be required for a restart run. These are .ckp, .mcmc, and infile.nex and any file with the format .run.t, or .run.p,
    where is either infile.nex (default) or any string specified by the command filename= in your Nexus block.
     
  3. One at a time, click the hyperlink for .ckp. When the file display page opens, look at the top of the page for the button "Save to Current Folder". Click that link. You will be prompted to specify a label for that file. Name the infile.nex.ckp, and submit. Alternatively, you can download all of the files as zip archive, and re-upload them together. This can be faster, and will only be problematic if some of the files are very large (like in the GB range).
     
  4. Repeat this process for each file, including .mcmc, and all files with the format .run.t, or .run.p. Be sure to preserve the numbers of the .t and .p files. So for example, .run1.t would become infile.nex.run1.t, and so forth.
     
  5. Once this process is complete, download the infile.nex file to your local machine, or edit it using the CIPRES interface, which now supports file editing. You must modify the file in two ways. First, in the mcmc command set in the MrBayes block, add the statement append=yes. Next, remove any filenames= commands in the MrBayes block. If your run stopped because your reached the maximum number of generations before the stoprule value was obtained, the number of generations ngen=... must be added or increased. If one forgets that, analysis will not restart.
     
  6. Upload the modified infile.nex to your work area.
     
  7. Now configure the job using the Restart Interface. Create a new Job. Select the modified infile.nex as the input file. Select the MrBayes 3.2.2 Restart as the Tool.

  8. Open the parameter pane, and select the files required for the restart, including infile.nex.ckp, infile.nex.mcmc, and any .t and .p files, such as infile.nex.run1.p, infile.nex.run1.t, etc

  9. Save the parameters, and start the run.

  10. Once the run begins, you will see in the "intermediate results" that two sets files will appear for each file you uploaded. For example, there will be an infile.nex.mcmc and an infile.nex.mcmc~ file. The file with the tilde (~) after it is a file created as part of the new run. The file without the tilde will be the file you uploaded, with the restart information appended to it.

We apologize for this very cumbersome process, but we wanted to expose this capability as soon as possible.

If the restart fails (thanks to Paula de Coito for this information):

1. Use the same sampling frequency as in the previous run to use relative burnin.

2. Check (and modify) the number in [generation: number] at line 3 of the .ckp file to match the previous number of generations in all the .p and .t files. This may happen if checkfreq was smaller than samplefreq.

For example, if one looks at the top of the ckp file for the above run one sees this:

#NEXUS
[ID: 7593968202]
[generation: 115894000]

But when you check the last generation in the t and p files for the same run it is 118500000
So one needs to change the generation number in the ckp file to match the last generation saved to the t and p file. (which it says to do in #2 above in red and can also be found on online fora). Once you do that the Restart Interface works perfectly.

3. Rarely, delete the last sample/line in the .p and .t files to achieve 2. above. This may happen if ngen was not divisible by samplefreq.

Known Issues: No known issues at present.

If there is a tool or a feature you need, let us know.

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