This is a test version of Biostars. For the public version, visit https://www.biostars.org.
MrBayes batch scripting

I wrote a nexus file with a mrbayes block for executing mrbayes in batch, but how can I get this script to execute as part of a workflow?

For example if I have a bash script that says

Execute example.nex

or 

mb

Execute example.nex

it doesn't work. How do I get mrbayes to execute autonomously?

mrbayes bash
• 3,800 views • link
updated by Mensur Dlakic Mensur Dlakic • written by DNAlias • DNAlias

Please explain "it doesn't work" (how it doesn't work? error messages?), and try to provide a simple example illustrating the issue. Did you read How do I run MrBayes in batch mode?

• 0 views • link
written by h.mon h.mon

1 answer

First you need to decide how you want to run MrBayes. If you type only mb (or mpirun -n #processors mb-mpi for multithreaded run), you are entering the interactive mode. It should give you a MrBayes > prompt. Once there, type execute example.nex and that will get things going unless there is an error. The program will tell you the exact line where the error occurred if something is wrong - you should report that message.

In command-line mode, you type:

mb example.nex > example.nex.log &

or

mpirun -n #processors mb-mpi example.nex > example.nex.log & (for MPI version)

• 0 views • link
written by Mensur Dlakic Mensur Dlakic

Log in to answer this question.

More posts like this