NullPointerException during initialization for UCRelaxedCladeClockModel

[J-Moravec]

NullPointerException during initialization for UCRelaxedCladeClockModel

[4ment]

Can you send me your xml files so I can debug it?

[J-Moravec]

Ah, sorry, I thought that I added it to the github post, but it does not accept XML files.

Here:
https://www.dropbox.com/s/t0tucvinwcmaklv/FlexibleLocalClock.xml?dl=0

I went through example XML and those old example XMLs that are downloaded with BEAST, but are no longer on github, but couldn't find why it isn't working. Clock, priors, operators and logs are all set up as in example files.

[4ment]

Sorry for the delay. I just had a look and it works for me with BEAST2.5. What is your BEAST version?

[J-Moravec]

2.5.2.
So my file works on your computer, but not mine? But examples are working on your and mine? I hate these mysteries.

Thanks, I would like to leave this open for a while until I figure out why it doesn't work or someone else can chip in with a similar problem.

[4ment]

Strange, what's the version of FLC in the package manager?

[J-Moravec]

1.1.0, what appears to be latest.

[4ment]

OK, I didn't realize that the XML you sent me actually worked because of the order of the taxa as you mentioned at the end of your first comment. If I select another set of taxa I get the same errors you described. The problem comes from SimpleRandomTree, it appears to be initialized differently from RandomTree.

As a quick fix you can replace this line
<init id="RandomTree.t:tree" spec="beast.evolution.tree.SimpleRandomTree" estimate="false" initial="@Tree.t:tree" taxa="@methylations"/>
with

<init id="RandomTree.t:tree" spec="beast.evolution.tree.RandomTree" estimate="false" initial="@Tree.t:tree" taxa="@methylations">
        <populationModel id="ConstantPopulation0.t:fluA" spec="ConstantPopulation">
            <parameter id="randomPopSize.t:fluA" name="popSize">1.0</parameter>
        </populationModel>
</init>