Phylogenetic Analysis: Parallel Mr. Bayes on a Cluster under SGE

mrbayes_sge.rst

Phylogenetic Analysis: Parallel Mr. Bayes on a Cluster under SGE

Mr. Bayes Block

begin mrbayes;
    charset CR = 1-732;
    charset cytB = 733-1846;
    charset struct = 1847-2716;
    [charset 12S  1847-2218;
     charset 16S 2219-2716; ]
    partition mtgenes = 3: CR, cytB, struct;
    set partition = mtgenes;
    exclude  1-160 211-260 364-384;
    lset applyto=(1,2,3) nst=6 rates=gamma;
    unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all);
    prset applyto=(all) ratepr=variable;
    mcmcp ngen=10000000 samplefreq=10000 printfreq=1000 nruns=4 nchains=4 mcmcdiagn=yes diagnfreq=1000000 burnin=200;
    mcmc burnin=200;
    sumt burnin=200;
    sump burnin=200;
end;

SGE Job Script

# /bin/sh
#$ -cwd
#$ -V
#$ -q "general.q"
#$ -pe mpi_general 8
#$ -l h_vmem=1G
#$ -l vf=1G
/opt/openmpi/bin/mpirun -np 8 /home/jeet/Environment/local/bin/mb-multi-3.2-cvs pythonidae.mb