Can't run beast

[HS]

I use Beast 2.1 in Windows. 

I can't run it.

It gives the following messages at the end

Start likelihood: Infinity after 11 initialisation attempts

P(posterior) = Infinity (was NaN)

P(prior) = Infinity (was NaN)

P(BayesianSkyline.t:Tree) = -1119.1238344397834 (was NaN)

P(MarkovChainedPopSizes.t:Tree) = -33.700856263602155 (was NaN)

P(KappaPrior.s:U7 1st and 2nd positions Ancients added) = -17.405609576780034 (was NaN)

P(KappaPrior.s:U7 3rd positions Ancients added) = -17.405609576780034 (was NaN)

P(KappaPrior.s:U7 control regions Ancients added) = -10.824714993076935 (was NaN)

P(HyperPrior.hyperNormal-mean-ucldStdevPrior.c:U7 1st and 2nd positions Ancients added) = 18.619131682676205 (was NaN)

P(HyperPrior.hyperNormal-mean-ucldStdevPrior.c:U7 3rd positions Ancients added) = Infinity (was NaN)

P(HyperPrior.hyperNormal-mean-ucldStdevPrior.c:U7 control regions Ancients added) = Infinity (was NaN)

P(HyperPrior.hyperNormal-sigma-ucldStdevPrior.c:U7 1st and 2nd positions Ancients added) = 0.0 (was NaN)

P(HyperPrior.hyperNormal-sigma-ucldStdevPrior.c:U7 3rd positions Ancients added) = 0.0 (was NaN)

P(HyperPrior.hyperNormal-sigma-ucldStdevPrior.c:U7 control regions Ancients added) = 0.0 (was NaN)

P(MeanRatePrior.c:U7 1st and 2nd positions Ancients added) = -3.6757541328186907 (was NaN)

P(MeanRatePrior.c:U7 3rd positions Ancients added) = -0.9189385332046732 (was NaN)

P(MeanRatePrior.c:U7 control regions Ancients added) = -1.8378770664093678 (was NaN)

P(ucldStdevPrior.c:U7 1st and 2nd positions Ancients added) = -1.0439385332046727 (was NaN)

P(ucldStdevPrior.c:U7 3rd positions Ancients added) = -1.0439385332046727 (was NaN)

P(ucldStdevPrior.c:U7 control regions Ancients added) = -1.0439385332046727 (was NaN)

P(U5s.prior) = NaN (was NaN)

P(U7s.prior) = NaN (was NaN)

P(U8s.prior) = NaN (was NaN)

P(Us.prior) = NaN (was NaN)

P(likelihood) = NaN (was NaN)

P(treeLikelihood.U7 1st and 2nd positions Ancients addeda) = NaN (was NaN)

P(treeLikelihood.U7 3rd positions Ancients added) = NaN (was NaN)

P(treeLikelihood.U7 control regions Ancients added) = NaN (was NaN)

java.lang.Exception: Could not find a proper state to initialise. Perhaps try another seed.

at beast.core.MCMC.run(Unknown Source)

at beast.app.BeastMCMC.run(Unknown Source)

at beast.app.beastapp.BeastMain.<init>(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

What I did incorrectly in Beauti?

Please help me to solve the problem.

I have run Beast 1.7 many times, and there was no such a problem.

Hovik

[Remco Bouckaert]

The output suggests that the prior called "HyperPrior.hyperNormal-mean-ucldStdevPrior.c:U7 3rd positions Ancients added" has zero probability. This can happen when the start value for the parameter for that the prior is outside the range of the distribution for that prior. To fix this, you can change the starting value so it is inside the distribution's range, or change the range of the distribution.

Note the same happens for "HyperPrior.hyperNormal-mean-ucldStdevPrior.c:U7 control regions Ancients added".

Let me know if this does not fix the problem,

Remco

[HS]

Hi Remco,

Thank you for your reply.

Unfortunately, I can't try your suggestions. My xml files have strange behavior. After some times when I open them, they have lost all parameter settings I had done. Most of them are with default settings. 

One more problem similar to that. When I wanted to reopen xml file with Beauti, it says an error (the same one which its said when I was trying to run beast) and doesn't open, although that file I made by beauty.

Best,

Hovik

[Remco Bouckaert]

Hi Hovik,

Perhaps you can send me the XML file, so I can investigate the problem.

Cheers,

Remco