Using R to do GMYC analysis

Yepp, trying hard to do a Gmyc analysis in R. Well thats not the problem, the problem is my mrbayes runs. They just run on and on for ever... when I had run the analysis for 2 hours and the standard deviation was down to 0.013, the clock just started increasing and this morning after running the analysis over night the estimated time left was about 5 hours...

#NEXUS[ Title UPGMA]begin data;
dimensions ntax= 101 nchar= 658;
format missing=? gap=- matchchar=. datatype=dna;
matrix

At the end of the nexus file:

Begin mrbayes;
set autoclose=yes;
lset nst=2 rates=invgamma;
prset Brlenspr=Clock:
uniform;mcmc ngen=1000000 samplefreq=1000;
end;