BEAST 2
Overview
BEAST (Bayesian Evolutionary Analysis Sampling Trees) is an application for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results.
Versions 2.6.7 and 2.7.0 are installed on the CSF.
Restrictions on use
BEAST 2 is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
Beast2 may be cited using the primary website: Bouckaert R.– BEAST 2.5 – https://www.beast2.org/citation/
Set up procedure
You will be able to access the executables by using one of the following module commands:
module load apps/binapps/beast2/2.7.0 module load apps/binapps/beast2/2.6.7
It is recommended loading modulefiles within your jobscript and let the job inherit these settings. Please do not run beast2 on the login node. Jobs should be submitted to the compute nodes via batch or run interactively, following the examples provided below.
Running the application
Example of interactively running BEAST2
module load apps/binapps/beast2/2.7.0 #reserving 2 cores qrsh -l short -pe smp.pe 2 beast testBSP.xml #or requesting for the v100 GPU qrsh -V -cwd -pe smp.pe 2 -l v100 beast testBSP.xml
Program descriptions and options are shown when running:
qrsh -l short -pe smp.pe 2 beast -help
Serial batch job submission
Create a batch submission script (which will load the modulefile in the jobscript), for example:
#!/bin/bash --login #$ -cwd # Job will run from the current directory ### You may need to add a high memory flag here e.g. #$ -l mem512 # Choose your required version module load apps/binapps/beast2/2.7.0 beast testBSP.xml
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
If you need more RAM (memory) to complete the analysis successfully, or you receive a similar error message with,
Error occurred during initialization of VM Could not reserve enough space for 8388608KB object heap
then please add the flags mentioned at the high-memory jobs page for more information.
Parallel batch job submission
Create a batch submission script (which will load the modulefile in the jobscript), for example:
#!/bin/bash --login #$ -cwd # Job will run from the current directory #$ -pe smp.pe 4 # Number of cores, can be 2--32 ### You may need to add a high memory flag here e.g. #$ -l mem512 # Choose your required version module load apps/binapps/beast2/2.7.0 # Need to add the "-thread" flag and # $NSLOTS will automatically set to the number of cores requested above beast -threads $NSLOTS testBSP.xml
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
If you need more RAM (memory) to complete the analysis successfully, and you may well do!, please add the flags mentioned at the high-memory jobs page for more information.
Further information
Updates
None.