I am trying to use MrBayes version 3.2.6 for phylogeny of several new nucleotide sequences. The sequences were aligned in ClustalX and the resulting Nexus files were edited to include the following code in the end:
end;
begin mrbayes;
outgroup SLA111mp11;
lset applyto=(all) nst=6 rates=gamma;
unlink shape=(all) pinvar=(all) statefreq=(all) revmat=(all);
prset applyto=(all) ratepr=variable;
set autoclose = yes;
mcmcp ngen=5500000 printfreq=1000 samplefreq=100
nchains=4 savebrlens=yes filename=test_output;
mcmc;
log start filename=test_output.log replace;
sumt filename=test_output.t burnin=5000 contype=halfcompat;
log stop;
end;
The file with complete code and sequences is attached.
When I execute the file in MrBayes, I invariably get a an error in the very end, saying "could not open file test_output.t. Error in command Sumt". Log file attached.
I tried different modifications to the SUMT line, but no success. Does anybody have an idea what exactly is wrong?
The output filename is wrongly formed delete the ".t" filename=test_output
see this modifed nexus file.
Thanks Csaba. The code finally works after having modified the output file name!
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