MrBayes Convergence issues ???

[ali zohaib]

Hello Everyone
Hope you are doing well

Actually, I am new to MrBayes, Before analysis of my data i am trying to replicate data from my reference paper (already published) just to compare my results. However, I am getting some convergence issues Please see the attached three pictures. Although when I used the MEGA6 ML tree convergence was same as expected. My aim is just to analyse by using Model "nst=6 rates=invgamma" 

I used two different blocks , 1st time (block 1) give less convergence and the second time  (2n dblock) give more however still the issue of Branch NC006430 remains it should resemble with the reference paper. Both blocks were used separately. 

Block 1

begin mrbayes;
set autoclose=yes nowarn=yes;
lset
nucmodel=4by4
nst=6
code=Universal
ploidy=Diploid
rates=Invgamma
ngammacat=4
nbetacat=5
omegavar=Equal
covarion=No
coding=All
parsmodel=No;
mcmcp
filename=siMBaoutput
nruns=2
nchains=4
swapfreq=1
samplefreq=500
printfreq=500
burninfrac=0.25
temp=0.1
nswap=1
mcmcdiagn=Yes
diagnfreq=5000
diagnstat=Avgstddev
savetrees=No
minpartfreq=0.1
allchains=No
allcomps=No
relburnin=Yes
burnin=0
stoprule=No
stopval=0.05
ordertaxa=No
ngen=1000000;
mcmc;
sump;

sumt
contype=halfcompat
conformat=Figtree;
end;

Block 2

begin mrbayes;

set autoclose=yes nowarn=yes;

lset nst=6 rates=invgamma;

mcmc ngen=1000000 relburnin=yes burninfrac=0.25 samplefreq=1000 printfreq=10000 nchains=4 savebrlens=yes;

sump burnin=2500;

sumt burnin=2500;

END;

Can you please suggest me how should I resolve the issue. I will be highly obliged.
 Looking forward for your kind response. 

MrBayes Convergence issues ??? - ResearchGate. Available from: https://www.researchgate.net/post/MrBayes_Convergence_issues [accessed Jan 22, 2016].