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