java.lang.NullPointerException: Cannot invoke "beast.base.evolution.tree.Node.getNr()" because "<local2>" is null

[forianfinest]

Hello there, I'm trying to run Coalescent Bayesian Skyline analysises with Beast 2.7.2 on Fedora 36, but it bugs with one of my files: java.lang.NullPointerException: Cannot invoke "beast.base.evolution.tree.Node.getNr()" because "<local2>" is null at beastlabs.evolution.tree.RNNIMetric.getCommonAncestor(Unknown Source) at beastlabs.evolution.tree.RNNIMetric.getCommonAncestor(Unknown Source) at beastlabs.evolution.tree.RNNIMetric.mrca(Unknown Source) at beastlabs.evolution.tree.RNNIMetric.distance(Unknown Source) at beastlabs.evolution.tree.RNNIMetric.distance(Unknown Source) at beast.base.evolution.operator.AdaptableOperatorSampler.computeSS(Unknown Source) at beast.base.evolution.operator.AdaptableOperatorSampler.accept(Unknown Source) at beast.base.inference.MCMC.propagateState(Unknown Source) at beast.base.inference.MCMC.doLoop(Unknown Source) at beast.base.inference.MCMC.run(Unknown Source) at beastfx.app.beast.BeastMCMC.run(Unknown Source) at beastfx.app.beast.BeastMain.main(Unknown Source) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.base/java.lang.reflect.Method.invoke(Unknown Source) at beast.pkgmgmt.launcher.BeastLauncher.run(Unknown Source) at beast.pkgmgmt.launcher.BeastLauncher.main(Unknown Source) I'm not sure what is the issue. I tried to run a Yule model with the same settings (mutation model and soft molecular clock) and it outputted correctly. I attach here the XML file (edited as a .txt file because GitHub does not allow to attach XML) nexus_edited.xml.txt . Thanks in advance for the suggestions on how to fix it. Best wishes, Mattia

[jordandouglas]

Hi, I was able to reproduce this issue using your xml file. There appears to be a bad interaction between the EpochFlexOperator and clock model. We are working on this issue now. In the meantime if you delete the 2 EpochFlexOperator objects from the xml file, or set their operator weights to 0, it should work fine.

[rbouckaert]

When running the analysis, population sizes seem to collapse to very small values. An alternative workaround is to keep the operators but set the lower bound on population sizes to a small value, so change the line

            <parameter id="bPopSizes.t:trimmed_acuto_all_modified" spec="parameter.RealParameter" dimension="5" lower="0" name="stateNode">380.0</parameter>

to

            <parameter id="bPopSizes.t:trimmed_acuto_all_modified" spec="parameter.RealParameter" dimension="5" lower="0.01" name="stateNode">380.0</parameter>

[zyy-1111]

I met a problem, could you heip me?

Restoring from file Fatal exception: Cannot invoke "beast.evolution.tree.Node.isLeaf()" because "" is null java.lang.NullPointerException: Cannot invoke "beast.evolution.tree.Node.isLeaf()" because "" is null at snap.likelihood.SnAPPrior.heightSum(Unknown Source) at snap.likelihood.SnAPPrior.heightSum(Unknown Source) at snap.likelihood.SnAPPrior.calculateLogP(Unknown Source) at beast.core.util.CompoundDistribution.calculateLogP(Unknown Source) at beast.core.util.CompoundDistribution.calculateLogP(Unknown Source) at beast.core.State.robustlyCalcPosterior(Unknown Source) at beast.core.MCMC.robustlyCalcPosterior(Unknown Source) at beast.inference.PathSamplingStep.run(Unknown Source) at beast.app.BeastMCMC.run(Unknown Source) at beast.app.beastapp.BeastMain.(Unknown Source) at beast.app.beastapp.BeastMain.main(Unknown Source) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:568) at beast.app.beastapp.BeastLauncher.run(Unknown Source) at beast.app.beastapp.BeastLauncher.main(Unknown Source) Fatal exception: Cannot invoke "beast.evolution.tree.Node.isLeaf()" because "" is null java.lang.RuntimeException: An error was encounted. Terminating BEAST at beast.app.util.ErrorLogHandler.publish(Unknown Source) at java.logging/java.util.logging.Logger.log(Logger.java:980) at java.logging/java.util.logging.Logger.doLog(Logger.java:1007) at java.logging/java.util.logging.Logger.log(Logger.java:1030) at java.logging/java.util.logging.Logger.severe(Logger.java:1777) at beast.app.beastapp.BeastMain.(Unknown Source) at beast.app.beastapp.BeastMain.main(Unknown Source) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:568) at beast.app.beastapp.BeastLauncher.run(Unknown Source) at beast.app.beastapp.BeastLauncher.main(Unknown Source)

Loading /tmp715/OneSp//step0/likelihood.logFile error: \tmp715\OneSp\step0\likelihood.log (系统找不到指定的文件。) java.lang.RuntimeException: An error was encounted. Terminating BEAST at beast.app.util.ErrorLogHandler.publish(Unknown Source) at java.logging/java.util.logging.Logger.log(Logger.java:980) at java.logging/java.util.logging.Logger.doLog(Logger.java:1007) at java.logging/java.util.logging.Logger.log(Logger.java:1030) at java.logging/java.util.logging.Logger.severe(Logger.java:1777) at beast.app.beastapp.BeastMain.(Unknown Source) at beast.app.beastapp.BeastMain.main(Unknown Source) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:568) at beast.app.beastapp.BeastLauncher.run(Unknown Source) at beast.app.beastapp.BeastLauncher.main(Unknown Source)