Path Sampling divide by zero error - workaround

[Brian Dorsey]

Hi all,

Beast 2.7.7

snapper 1.1.4

Mac Studio M1 Ultra

I'm trying to set up a snapper path sampling analysis but I am getting an error. When executing the path sampling xml file, program quits with the dividing by zero error pasted below. I think I've traced it to this line in the beast.xml files created in each step folder:

 <logger id="Logger" spec="Logger" fileName="likelihood.log" logEvery="0">
            <log idref="likelihood"/>
        </logger>

If I modify this element to logEvery="10" and then run the run0.sh script in the folder containing the step folders, the error is gone. So I guess the Path Sampler module is writing the likelihood log element incorrectly. I can edit each beast.xml file and go from there but maybe there is a better fix. In any case, I thought folks would want to know about this in case they get the same error. Happy to provide more info if it would be helpful.

Thanks,

Brian D.

Start likelihood: -3519.4399537669206
Writing file alignment.1720737038787.log
         Sample      posterior ESS(posterior)     likelihood          prior
Writing file alignment.1720737038787.trees
Writing file likelihood.log
              0     -1815.6024              N     -1818.7203         3.1178 --
java.lang.ArithmeticException: / by zero
at beast.base.inference.Logger.log(Unknown Source)
at beast.base.inference.MCMC.log(Unknown Source)
at modelselection.inference.PathSamplingStep.doLoop(Unknown Source)
at modelselection.inference.PathSamplingStep.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)
java.io.FileNotFoundException: /Volumes/CatDisk/Dioon_RADseq_analysis/Dtom/phylo/analyses/snapper/bfd/example/step0/beast.xml.state (No such file or directory)
at java.base/java.io.FileInputStream.open0(Native Method)
at java.base/java.io.FileInputStream.open(Unknown Source)
at java.base/java.io.FileInputStream.<init>(Unknown Source)
at modelselection.inference.PathSampler.copyStateFile(Unknown Source)
at modelselection.inference.PathSampler.doRuns(Unknown Source)
at modelselection.inference.PathSampler.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)