Dear Denise, Why did initialising errors always occurred if I chose either BDSKY(contempory) or BDSIR(contempory)

[bioz...@gmail.com]

Dear Denise,

 

Would you mind check my two xml files as attchments (They are separately created by  choosing the BDSKY BDSKY(contempory)  and BDSIR(contempory) respectively ). Two similar initialise errors always ocurred when ran the two xml file. The error prompt as follows:

 

The error for BDSKY:

-------------------------------------------------------------------------------------------------------------------------------

Start likelihood: -Infinity after 11 initialisation attempts
P(posterior) = -Infinity (was NaN)
 P(prior) = -Infinity (was NaN)
  P(BirthDeathSkyContemporary.t:Clade3) = -Infinity (was NaN)
  P(R0Prior.t:Clade3) = -16.30738630443746 (was NaN)
  P(becomeUninfectiousRatePrior.t:Clade3) = -9.189385332046724 (was NaN)
  P(ClockPrior.c:Clade3) = 0.0 (was NaN)
  P(origRootPrior.t:Clade3) = -6.907755278982137 (was NaN)
  P(RateACPrior.s:Clade3) = -3.184008455701433 (was NaN)
  P(RateAGPrior.s:Clade3) = -3.1686658147294304 (was NaN)
  P(RateATPrior.s:Clade3) = -3.184008455701433 (was NaN)
  P(RateCGPrior.s:Clade3) = -3.184008455701433 (was NaN)
  P(RateGTPrior.s:Clade3) = -3.184008455701433 (was NaN)
  P(rhoPrior.t:Clade3) = 8.881784197001248E-16 (was NaN)
 P(likelihood) = NaN (was NaN)
  P(treeLikelihood.Clade3) = 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)

-------------------------------------------------------------------------------------------------------------------------------

 

The error for BDSIR:

-------------------------------------------------------------------------------------------------------------------------------

Start likelihood: -Infinity after 11 initialisation attempts
P(posterior) = -Infinity (was NaN)
 P(prior) = -Infinity (was NaN)
  P(BDSIRcontemp.t:Clade3) = -Infinity (was NaN)
  P(R0PriorEc.t:Clade3) = -1.9889742295326522 (was NaN)
  P(S0_priorEc.t:Clade3) = -16.88190852405692 (was NaN)
  P(becomeUninfectiousRatePriorEc.t:Clade3) = -0.9189385332046727 (was NaN)
  P(ClockPrior.c:Clade3) = 0.0 (was NaN)
  P(origRootPriorEc.t:Clade3) = -6.907755278982137 (was NaN)
  P(RateACPrior.s:Clade3) = -3.184008455701433 (was NaN)
  P(RateAGPrior.s:Clade3) = -3.1686658147294304 (was NaN)
  P(RateATPrior.s:Clade3) = -3.184008455701433 (was NaN)
  P(RateCGPrior.s:Clade3) = -3.184008455701433 (was NaN)
  P(RateGTPrior.s:Clade3) = -3.184008455701433 (was NaN)
  P(rhoPriorEc.t:Clade3) = 8.881784197001248E-16 (was NaN)
 P(likelihood) = NaN (was NaN)
  P(treeLikelihood.Clade3) = 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)

-------------------------------------------------------------------------------------------------------------------------------

 

However,  if we chose the corresponding two priors with the time serial sampling, the runs would be ok.

 

So please check my two xml files and give me some suggestions, Thanks very much!

 

Cheers,

 

Jie

[Denise]

Dear Jie,

You're assuming that all taxa were sampled at present (that's the default for contemporaneous sampling). Hence, the probability of having any samples before present is zero. But your sampling dates differ from one another, i.e. they are not all sampled at present, which is why the treePrior returns -Infinity. 

Kind regards

Denise

[Jie Zha]

Dear Denise,

Than you for your suggestions very much. I have understood what caused the errors. I guess if I edit the xml file to BDSKY (contemporary) or BDSIR(contemporary) by adding multiple rho sampling events,  the run will be ok. 

However, after the respective BDSKY (contemporary) xml file was edited, another error occurred. Please see the detail description at:

https://groups.google.com/forum/#!topic/beast-users/_XMHCNNKwzA ,which was in my further reply to you in the post.

 

Thanks your time again!

 

Looking forward to recive you again!

 

Cheers,

 

Jie

 

 

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