Running beast on linux

Brad

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Dec 9, 2017, 3:33:40 AM12/9/17

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Hello,

I seem to be getting an error while trying to run beast on our linux cluster. I've attached my .xml file if that may help. Below is the error I receive:

Writing file Location_tree_with_trait.trees

Sample posterior ESS(posterior) likelihood prior

Fatal exception: null

java.lang.NullPointerException

at beast.evolution.likelihood.AncestralStateTreeLikelihood.getStates(Unknown Source)

at beast.evolution.likelihood.AncestralStateTreeLikelihood.traverseSample(Unknown Source)

at beast.evolution.likelihood.AncestralStateTreeLikelihood.redrawAncestralStates(Unknown Source)

at beast.evolution.likelihood.AncestralStateTreeLikelihood.getStatesForNode(Unknown Source)

at beast.evolution.likelihood.AncestralStateTreeLikelihood$1.getTraitString(Unknown Source)

at beast.evolution.tree.TreeWithTraitLogger.toNewick(Unknown Source)

at beast.evolution.tree.TreeWithTraitLogger.log(Unknown Source)

at beast.core.Logger.log(Unknown Source)

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

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

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

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)

Fatal exception: null

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

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

at java.util.logging.Logger.log(Logger.java:738)

at java.util.logging.Logger.doLog(Logger.java:765)

at java.util.logging.Logger.log(Logger.java:788)

at java.util.logging.Logger.severe(Logger.java:1463)

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

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

Any help would be greatly appreciated. Thanks!

Brad

1.xml

Remco Bouckaert

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Dec 10, 2017, 5:07:21 PM12/10/17

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Hi Brad,

I had no problem running the file you posted (for the first million states at least). Which version of BEAST 2 and BEAST_CLASSIC are you using on the cluster? You could try updating to the latest version.

Cheers,

Remco

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<1.xml>

Remco Bouckaert

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Dec 10, 2017, 5:07:21 PM12/10/17

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