Problem in stepping stone method by path sampler(app)

[Rubayetul Alam]

I have found this problem when running with the praticular tree prior model. I have changed the operator value of "delta exchange" but it did not work. Is there any problem in the parameter value?

Thanks in advance.

Restoring from file

Start likelihood: -Infinity 

P(posterior) = -Infinity (was NaN)  **

P(prior) = -Infinity (was NaN)  **

P(ExtendedBayesianSkyline.t:Final dataset_FMDV_Asia1) = -Infinity (was NaN)  **

P(GammaShapePrior.s:Final dataset_FMDV_Asia1) = -1.448 (was NaN)  **

P(indicatorsPrior.alltrees) = -0.69314718056 (was NaN)  **

P(popSizePrior.alltrees) = -146.0 (was NaN)  **

P(populationMeanPrior.alltrees) = 0.0 (was NaN)  **

P(PropInvariantPrior.s:Final dataset_FMDV_Asia1) = 0.0 (was NaN)  **

P(RateACPrior.s:Final dataset_FMDV_Asia1) = -3.184008455701433 (was NaN)  **

P(RateAGPrior.s:Final dataset_FMDV_Asia1) = -3.1686658147294304 (was NaN)  **

P(RateATPrior.s:Final dataset_FMDV_Asia1) = -3.184008455701433 (was NaN)  **

P(RateCGPrior.s:Final dataset_FMDV_Asia1) = -3.184008455701433 (was NaN)  **

P(RateGTPrior.s:Final dataset_FMDV_Asia1) = -3.184008455701433 (was NaN)  **

P(MeanRatePrior.c:Final dataset_FMDV_Asia1) = 0.0 (was NaN)  **

P(ucldStdevPrior.c:Final dataset_FMDV_Asia1) = 0.819364145120802 (was NaN)  **

P(likelihood) = NaN (was NaN)  **

P(treeLikelihood.Final dataset_FMDV_Asia1) = NaN (was NaN)  **

Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.

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

at beast.inference.PathSamplingStep.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)

Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.

java.lang.RuntimeException: An error was encounted. Terminating BEAST

at beast.app.util.ErrorLogHandler.publish(Unknown Source)

at java.util.logging.Logger.log(Unknown Source)

at java.util.logging.Logger.doLog(Unknown Source)

at java.util.logging.Logger.log(Unknown Source)

at java.util.logging.Logger.severe(Unknown Source)

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

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

Loading /tmp/step0/likelihood.log, burnin 50%, skipping 500 log lines

|---------|---------|---------|---------|---------|---------|---------|---------|

***********************************************************************************

Calculating statistics

|---------|---------|---------|---------|---------|---------|---------|---------|

********************************************************************************

marginalLs[0 ] = -14407.128347275051

\tmp\step1\likelihood.log (The system cannot find the file specified)

[Remco Bouckaert]

It looks like the ExtendedBayesianSkyline restores to a value that is -Infinity. There was a fix not too long ago for restoring coalescent likelihoods from file, so perhaps upgrading to the latest version of BEAST may help.

Remco

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