BEAST2¶
BEAST2 is a tool for Bayesian phylogenetic analysis.
Is BEAST2 a new version of BEAST?
No.
Although BEAST and BEAST2 achieve a similar goal, BEAST and BEAST2 are developed independently.
Hence:
- there are things BEAST can do that BEAST2 cannot, and vice versa
- one cannot create a BEAST XML file and expect BEAST2 to be able to run it, and vice versa
Using BEAST2¶
Here is how to use BEAST2 on the UPPMAX clusters.
Prefer a video?
This YouTube video shows how to use BEAST2 on the UPPMAX clusters.
1. Load a beast2
module¶
First step is to load a BEAST2 module.
Here is how to find the BEAST2 versions on the UPPMAX clusters:
When loading a BEAST2 module, also load bioinfo-tools
:
How does that look like?
$ module load bioinfo-tools beast2/2.7.4
beast2/2.7.4: Also loaded beagle/4.0.0
beast2/2.7.4: Many Beast packages are available, to see the list, 'packagemanager -list'
beast2/2.7.4: Use BEAST_XMX to specify the amount of RAM (default 5g), 'export BEAST_XMX=15g'. Do not exceed RAM available to your job.
2. Run BEAUti
¶
Next step is to create a BEAST2 configuration file
using BEAUti
. This graphical tool can be started using:
As BEAUti
is a graphical program,
it needs SSH with X forwarding enabled enabled.
How does that look like?
Starting BEAUti
results in the following pop-up window:
After using BEAUti
, save the file with your BEAST2 model.
3. Run¶
A BEAST2 run takes a lot of computing power, hence do not run it on a login node. Instead, run it on an interactive node or use a script.
How to start an interactive node?
View the UPPMAX documentation 'How to start an interactive node on Rackham'.
On an interactive node, run BEAST2 on the saved BEAST2 model:
When using a script, put that line in a script.
Below is an example script, called run_beast2.sh
:
#!/bin/bash
#SBATCH -A uppmax2023-2-25
module load bioinfo-tools beast2/2.7.4
beast beast2_setup.xml
- In line 2, replace
uppmax2023-2-25
with your UPPMAX project. - In line 3, you may want to replace
beast2/2.7.4
with your favorite BEAST2 version
Then run this script using sbatch run_beast2.sh
.
Note that this is a minimal script. See the UPPMAX documentation on Slurm for ways to improve this script.
View the trees using DensiTree¶
DensiTree is a tool that allows one to display the posterior tree distribution of a BEAST2 run.
Run:
where [trees_filename]
is the name of the file containing the posterior trees,
resulting in, for example, densitree my_file.trees
.
Run Tracer¶
Tracer is a tool to analyse the results of a (BEAST or) BEAST2 run.
Show info¶
How does that look like?
Here the command is run on a Rackham compute node, using an interactive session.
Here an interactive session with 1 node:
[sven@s93 ~]$ beast -beagle_info
BEAST v2.7.4, 2002-2023
Bayesian Evolutionary Analysis Sampling Trees
Designed and developed by
Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard
Centre for Computational Evolution
University of Auckland
r.bouckaert@auckland.ac.nz
alexei@cs.auckland.ac.nz
Institute of Evolutionary Biology
University of Edinburgh
a.rambaut@ed.ac.uk
David Geffen School of Medicine
University of California, Los Angeles
msuchard@ucla.edu
Downloads, Help & Resources:
http://beast2.org/
Source code distributed under the GNU Lesser General Public License:
http://github.com/CompEvol/beast2
BEAST developers:
Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled,
Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li,
Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel,
Oliver Pybus, Tim Vaughan, Chieh-Hsi Wu, Walter Xie
Thanks to:
Roald Forsberg, Beth Shapiro and Korbinian Strimmer
--- BEAGLE RESOURCES ---
0 : CPU (x86_64)
Flags: PRECISION_SINGLE PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL EIGEN_COMPLEX SCALING_MANUAL SCALING_AUTO SCALING_ALWAYS SCALERS_RAW SCALERS_LOG VECTOR_SSE VECTOR_NONE THREADING_CPP THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU
Here an interactive session with 2 nodes:
[sven@s106 ~]$ beast -beagle_info
BEAST v2.7.4, 2002-2023
Bayesian Evolutionary Analysis Sampling Trees
Designed and developed by
Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard
Centre for Computational Evolution
University of Auckland
r.bouckaert@auckland.ac.nz
alexei@cs.auckland.ac.nz
Institute of Evolutionary Biology
University of Edinburgh
a.rambaut@ed.ac.uk
David Geffen School of Medicine
University of California, Los Angeles
msuchard@ucla.edu
Downloads, Help & Resources:
http://beast2.org/
Source code distributed under the GNU Lesser General Public License:
http://github.com/CompEvol/beast2
BEAST developers:
Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled,
Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li,
Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel,
Oliver Pybus, Tim Vaughan, Chieh-Hsi Wu, Walter Xie
Thanks to:
Roald Forsberg, Beth Shapiro and Korbinian Strimmer
--- BEAGLE RESOURCES ---
0 : CPU (x86_64)
Flags: PRECISION_SINGLE PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL EIGEN_COMPLEX SCALING_MANUAL SCALING_AUTO SCALING_ALWAYS SCALERS_RAW SCALERS_LOG VECTOR_SSE VECTOR_NONE THREADING_CPP THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU
Troubleshooting¶
BEAUti gives BadAlloc
¶
- Platform(s): MacOS
This problem seems to be related to not having a proper X server installed.
In this case, SSH X forwarding works to the extent
that SSH is able to show xeyes
, yet fails to show BEAUti.
Also, using the remote desktop via a ThinLinc client fails.
A solution may be to use the remote desktop via the web
How does that look like?
Here is how it looks like:
[kayakhi@rackham2 ~]$ xeyes
[kayakhi@rackham2 ~]$ module load bioinfo-tools beast2/2.7.4
beast2/2.7.4: Also loaded beagle/4.0.0
beast2/2.7.4: Many Beast packages are available, to see the list, 'packagemanager -list'
beast2/2.7.4: Use BEAST_XMX to specify the amount of RAM (default 5g), 'export BEAST_XMX=15g'. Do not exceed RAM available to your job.
[kayakhi@rackham2 ~]$ beauti
X Error of failed request: BadAlloc (insufficient resources for operation)
Major opcode of failed request: 149 (GLX)
Minor opcode of failed request: 5 (X_GLXMakeCurrent)
Serial number of failed request: 0
Current serial number in output stream: 32
Note that this user has enabled SSH X forwarding,
as is proven by calling xeyes
without problems.