Population model is deleted after splitting an alignment in Beauti Starbeast2 Template

Alexis Sullivan

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Mar 31, 2017, 6:19:04 AM3/31/17

to beast-users

Hi,

I'm trying to use the Starbeast2 template but am encountering an error in when creating the template in BEAUTI. When I split a data alignment into partitions, the 'Population Model' tab changes from the model selection drop-down box to a empty page that says "No Input Editors." This happens if I run any of the clock models but doesn't happen in regular StarBEAST. I'm using BEAST2 v2.4.5 and running Windows 10.

If I try to run the xml anyway, I get this error message:

Error 110 parsing the xml input file

validate and intialize error: Input 'childModel' must be specified.

Error detected about here:

<beast>

java.lang.IllegalArgumentException: Input 'childModel' must be specified.

at beast.core.Input.validate(Unknown Source)

at beast.core.BEASTInterface.validateInputs(Unknown Source)

at beast.util.XMLParser.createObject(Unknown Source)

at beast.util.XMLParser.parseInputs(Unknown Source)

at beast.util.XMLParser.createObject(Unknown Source)

at beast.util.XMLParser.parseInputs(Unknown Source)

at beast.util.XMLParser.createObject(Unknown Source)

at beast.util.XMLParser.parseRunElement(Unknown Source)

at beast.util.XMLParser.parse(Unknown Source)

at beast.util.XMLParser.parseFile(Unknown Source)

at beast.app.BeastMCMC.parseArgs(Unknown Source)

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

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

Am I making a mistake here? Or is this a bug?

Huw A. Ogilvie

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Mar 31, 2017, 7:00:46 AM3/31/17

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Hi Alexis, this is a bug. Thanks for reporting it here, it will be fixed in the next version of StarBEAST2.

In the mean time, you can fix the XML by finding the following line:

<populationModel id="popModelBridge.Species" spec="starbeast2.PassthroughModel"/>

and replacing it with this:

Huw A. Ogilvie

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Mar 31, 2017, 7:47:05 AM3/31/17

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Actually it turns out the tree prior gets deleted as well whenever a partition is split or deleted. So you might have to hold on til the next version of StarBEAST2.

Huw A. Ogilvie

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Mar 31, 2017, 9:05:34 AM3/31/17

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Okay this is now fixed in version 0.13.5. It might take a while for this to appear in BEAUTi, but you can update StarBEAST2 manually by downloading it from here:

https://github.com/genomescale/starbeast2/releases

And following the instructions from here:

http://www.beast2.org/managing-packages/#Install_by_hand

Ian Brennan

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May 15, 2018, 4:57:29 AM5/15/18

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Huw, just a heads up, this is still an issue in BEAUTi v2.5.0 Java version 1.8.0_102 with StarBEAST2 0.14.1. I haven't tried your suggestion of a manual install of StarBEAST2, but instead partitioned my morphological data into separate files by number of states and that worked.