Handling of returned MrBayes files

Mark Miller

• June 27, 2016 05:14

Hi,

I am currently able to submit a MrBayes job via the plugin I made myself which somewhat resembles the existing MrBayes plugin. However, I am stuck on how to create and display the returned parameters. From the submission, I am able to retrieve the following parameters:

1. infile.nex (283 bytes )
2. _scheduler_stderr.txt (663 bytes )
3. scheduler.conf (66 bytes )
4. start.txt (40 bytes )
5. _JOBINFO.TXT (332 bytes )
6. term.txt (379 bytes )
7. paramfile.txt (1170 bytes )
8. stderr.txt (0 bytes )
9. stdout.txt (4296 bytes )
10. done.txt (40 bytes )
11. STDOUT (4296 bytes )
12. STDERR (0 bytes )

So can someone direct me to the appropriate documentations on how to display these outputs on Geneious?

 

Thank you very much,
Mark

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  Richard Moir

  • June 27, 2016 08:12

  Hi Mark,

  I don't see any of the usual MrBayes output files in your list there. Usually there are .mcmc, .p and .t  files. STDOUT looks quite big, is there anything in there? Check that MrBayes actually ran to completion correctly if you can.

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  Mark Miller

  • June 29, 2016 18:23

  Yes, successful files include .t, .p, and .mcmc. There are also tree files, which include .trprobs and .con,  checkpoint file for restart .ckp and these:

  .parts

  .pstat

  .tstat

  .vstat

  .lstat

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  Richard Moir

  • June 29, 2016 22:40

  The files that contain trees can be imported using NexusImporter from Jebl easily enough, the other files are trickier. Our MrBayes plugin uses Tracer (http://beast.bio.ed.ac.uk/Tracer) to do all the visualization which is bundled with the plugin. We parse this data out of the .p file and store it in xml then pass it to Tracer. Unfortunately all of this is internal to our plugin so you can't access it from yours.

   

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