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PhyloBayes MPI on XSEDE RESTART (v 1.4f)

This interface allows a user to restart a PhyloBayes (Lartillot et al, 2009) run, so long as the files produced were not corrupted. The interface is a bit cumbersome and fragile today, but it will work. We hope to have a more elegant version in the near future. To use this interface follow these steps:

Go to the results of the run you wish to restart. Identify the following files in your results:

• chain0.chain: and all similarly named .chain files.
• chain0.treelist: and all similarly named .treelist files.
• chain0.trace: and all similarly named .trace files.
• chain0.param and all similarly named .param files.
• chain0.monitor and all simialrly named .monitor files

The number of each file type will be equal to the number of chains in the run you attempting to restart. This number will be 2,3, or 4 (more than 4 chains are not currently allowed). The number following chain in the prefix (0,1,2, or 3) identifies which of the chains this file belongs to. So any file beginning with "chain0" belongs to the first chain, those with "chain1" belong to the second chain,and so forth. There will be five files for each chain you wish to restart.

You must now manually move each of these output files to your data area (sorry about that). For each of those files, click the "View" button. When the new page opens, find the button at the top of the page that says "Save to Current Folder". When the new page opens, name the file something that will help you identify it (for example, preserve the prefix with the number of the chain it belongs to), and save. Repeat this procedure for each of the .phy, .chain, .trace, .treelist, and .param files. Each of the files belongs to the "chain" files with the same number, so it is important to name the files in easily recognizable ways. Once you have saved all of them to your current work folder, create a task using the PhyloBayes MPI on XSEDE Restart interface. Select the .phy file for the run you are restarting as input.

Open the parameter pane. Select the correct number of chains for the run you are restarting. Scroll down in the interface and use the drop-down boxes to select the correct .chain, .trace, .treelist, and .param files for your run. Be sure to match each of these to the correct chain, using the files original chain0, chain1, chain2, and chain3. Save your job, and run.

Please contact us if you have trouble using the interface.

 

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