MrBayes-Sapelo2
Category
Bioinformatics
Program On
Sapelo2
Version
3.2.6, 3.2.7a
Author / Distributor
Fredrik Ronquist, School of Computational Science, Florida State University, ronquist@csit.fsu.edu
John P. Huelsenbeck, Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, johnh@biomail.ucsd.edu
Description
MrBayes (Bayesian Analysis of Phylogeny)
MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. It uses Markov chain Monte Carlo (or CMC) to approximate the posterior probabilities of trees.
Running Program
Also refer to Running Jobs on Sapelo2
- Version 3.2.6 is installed in /apps/eb/MrBayes/3.2.6-foss-2019b/
To use this version of MrBayes, please first load the module with
module load MrBayes/3.2.6-foss-2019b
- Version 3.2.7a is installed in /apps/eb/MrBayes/3.2.7a-foss-2019b/
To use this version of MrBayes, please first load the module with
module load MrBayes/3.2.7a-foss-2019b
Note that this version of MrBayes does not work on the AMD Opteron processors. When using this version, please add the option --constraint=EDR to exclude the Opteron processors. For example, add the following line to your job submission script:
#SBATCH --constraint=EDR
Sample script subp.sh to run in the batch queue asking for 18 cores:
#!/bin/bash #SBATCH --job-name=mrbayes # Job name #SBATCH --partition=batch # Partition (queue) name #SBATCH --constraint=EDR # node feature #SBATCH --nodes=2 # Number of nodes #SBATCH --ntasks=18 # Number of MPI ranks #SBATCH --ntasks-per-node=9 # How many tasks on each node #SBATCH --cpus-per-task=1 # Number of cores per MPI rank #SBATCH --mem-per-cpu=600mb # Memory per processor #SBATCH --time=24:00:00 # Time limit hrs:min:sec #SBATCH --output=%x.%j.out # Standard output log #SBATCH --error=%x.%j.err # Standard error log #SBATCH --mail-type=ALL # Mail events (NONE, BEGIN, END, FAIL, ALL) #SBATCH --mail-user=username@uga.edu # Where to send mail cd $SLURM_SUBMIT_DIR module load MrBayes/3.2.7a-foss-2019b mpirun $EBROOTMRBAYES/bin/mb < input.par
where 'input.par' needs to be replaced by the input file that you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the job name need to be modified appropriately as well.
Then submit job to the queue as
sbatch ./subp.sh
Documentation
http://mrbayes.csit.fsu.edu/wiki/index.php/Manual
Installation
Source code downloaded from http://mrbayes.csit.fsu.edu/
System
64-bit Linux