Questions about estimation of the average standard deviation of split frequencies in MrBayes

[daniel yao]

Hi everyone,

I'm sorry if I posted my questions in unsuitable place. Perhaps, I should ask this question in the Google Group of MrBayes if it existed. But I thought that people who use BUCKy might also meet similar problem previously. 

I tried to use the MrBayes for the BUCKy analysis, and sequence alignment of my whole SNP was chunked into hundreds of subsets with 10,000 bp SNPs. The sequence alignment was from 31 individuals that belonged to multiple species. I ran the MrBayes version 3.2.7a on centos7 system. But when the MrBayes analysis was going, every diagnfreq displayed "Average standard deviation of split frequencies: NA (no splits above min. frequency)". Originally, I thought that it might be because the number of generation was not long enough. Then, I set the ngen to 21,000,000. It still displayed "Average standard deviation of split frequencies: NA (no splits above min. frequency)". My questions are:

1. Are results from this MrBayes analysis reliable that can be used for BUCKy analysis?

2. If the results are not reliable, how should I do to improve my MrBayes analysis? For example, should I change the lset, nchains, or other parameters in the block?

Here is the block file I used.

"""

#nexus

begin mrbayes;

set autoclose=yes nowarn=yes;

execute 10kb_92_subalignment.nex;

lset nst=6 rates=gamma;

prset brlenspr=Unconstrained:Exp(50.0);

mcmc nruns=2 temp=0.2 ngen=21000000 burninfrac=0.1909

Nchains=4 samplefreq=1000 swapfreq=1000 printfreq=50000

mcmcdiagn=yes diagnfreq=50000 filename=10kb_92;

quit;

end;

"""

This block file was edited basing on the BUCKy tutorial. I also searched similar questions in the Google Group of the BUCKy here and other websites in Google, but I didn't find useful information. I appreciate if anyone knows what I should do about my questions. Thank you.

Best regards,

Xin