Thorney Likelihood - Template File

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Conor O'Hare

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Sep 29, 2024, 2:30:07 PM9/29/24
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Hi all,

I am trying to adapt my dataset to this method of analysis. I have constructed the branch length tree using RAxML, and the time-calibrated tree using the R package treedater.

Following as best I could to adapt the xml file, I received the error:

SEVERE:
******
Error in input BEAST XML file, D4_NEA_GISAID.xml:
The '<thorneyTreeLikelihood>' element, with id, 'treeLikelihood', is incorrectly constructed.
The following was expected:
Exactly one ELEMENT of type MutationBranchMap REQUIRED
******

To check how it should function, I tried running the template file given on BEAST, found at the end of the tutorial (and linked here). But doing that without any adaptions gives this:

SEVERE: Parsing error - poorly formed BEAST file, template.xml:
Object with idref=treeModel has not been parsed.

Error thrown at: dr.xml.XMLParser.convert(Unknown Source)

Ignoring for now my own data, I am curious if I should be able to run this template without any changes? My thinking is that once I see how this works, I can use this to run for my sequences.

Thanks!
Conor

Alberto Aguayo

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Oct 6, 2024, 2:27:36 PM10/6/24
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Hello, did someone already know the answer for these errors?, currently I have the same issue and don't clue of whats going on, I do the tutorial too with the same results.

 SEVERE: Parsing error - poorly formed BEAST file, template.xml:
Object with idref=treeModel has not been parsed.

Also I already try different BEAST version but similar results has been emerge:

 BEAST v1.10.5 Prerelease

Failed to load parser: New parser (gmrfSkygridBlockUpdateOperator) in {interface dr.inference.operators.MCMCOperator} cannot replace existing parser (gmrfSkygridBlockUpdateOperator) in {interface dr.inference.operators.MCMCOperator}
line = dr.evomodelxml.coalescent.operators.GMRFSkygridBlockUpdateOperatorParser


Failed to load parser: dr.evomodelxml.coalescent.GMRFTestLikelihoodParser
line = dr.evomodelxml.coalescent.GMRFTestLikelihoodParser



Failed to load parser: dr.inference.trace.DnDsPerSiteAnalysis
line = dr.inference.trace.DnDsPerSiteAnalysis


Failed to load parser: dr.inference.trace.CnCsPerSiteAnalysis
line = dr.inference.trace.CnCsPerSiteAnalysis


Failed to load parser: dr.inference.trace.CnCsToDnDsPerSiteAnalysis
line = dr.inference.trace.CnCsToDnDsPerSiteAnalysis

Loading additional development parsers from development_parsers.properties, which is additional set of parsers only available for development version ...


Failed to load parser: dr.evomodel.continuous.hmc.TaskPool
line = dr.evomodel.continuous.hmc.TaskPool


Failed to load parser: dr.inferencexml.operators.RepeatOperatorParser
line = dr.inferencexml.operators.RepeatOperatorParser

Parsing XML file: V.1.10.4Tutorial_tbeast_NonR_test.xml
  File encoding: UTF8
Looking for plugins in /Users/albertoaguayoacosta/plugins
Using node heights.

Creating the constrained tree model based on big fast tree model, 'treeModel'
  taxon count = 89
  tree height = 1.2208646178755767
The gmrfSkyrideLikelihood has time aware smoothing
Creating a GMRF smoothed skyride model for multiple loci (SkyGrid)
Population sizes: 36
Oct 03, 2024 4:36:33 PM dr.app.beast.BeastMain <init>
SEVERE: Parsing error - poorly formed BEAST file, V.1.10.4Tutorial_tbeast_NonR_test.xml:

The '<thorneyTreeLikelihood>' element, with id, 'treeLikelihood', is incorrectly constructed.
The following was expected:
Exactly one ELEMENT of type ThorneyBranchLengthLikelihoodDelegate REQUIRED

Error thrown at: dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)





 BEAST X v10.5.0-beta4

Error in input BEAST XML file, V.1.10.4Tutorial_tbeast_NonR_test.xml:

The '<thorneyTreeLikelihood>' element, with id, 'treeLikelihood', is incorrectly constructed.
The following was expected:
Exactly one ELEMENT of type MutationBranchMap REQUIRED




 BEAST v1.10.4 Prerelease

SEVERE: Parsing error - poorly formed BEAST file, V.1.10.4Tutorial_tbeast_NonR_test.xml:

Object with idref=treeModel has not been parsed.

Error thrown at: dr.xml.XMLParser.convert(Unknown Source)



Hope someone could help. Beast regards

Alberto Aguayo

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Oct 6, 2024, 2:27:36 PM10/6/24
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Hello I currently try to use thorney-BEAST for the analysis of SARS-CoV-2 samples, and i followed the instructions in the [thorney_beast.xml] document to create my XML file. However when I try to running in BEAST the following error messages appear:

SEVERE: Parsing error - poorly formed BEAST file, V.1.10.4Tutorial_tbeast_NonR_test.xml:

The '' element, with id, 'treeLikelihood', is incorrectly constructed.


The following was expected:
Exactly one ELEMENT of type ThorneyBranchLengthLikelihoodDelegate REQUIRED

Error thrown at: dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)

BEAST X v10.5.0-beta4

Error in input BEAST XML file, V.1.10.4Tutorial_tbeast_NonR_test.xml:

The '' element, with id, 'treeLikelihood', is incorrectly constructed.


The following was expected:
Exactly one ELEMENT of type MutationBranchMap REQUIRED

BEAST v1.10.4 Prerelease

SEVERE: Parsing error - poorly formed BEAST file, V.1.10.4Tutorial_tbeast_NonR_test.xml:
Object with idref=treeModel has not been parsed.

Error thrown at: dr.xml.XMLParser.convert(Unknown Source)

Could some one explain how to fixed the XML file? or if there is another previews step that is requiered to do?

Many thanks

Vanise de Medeiros

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Oct 21, 2024, 6:01:53 PM10/21/24
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Hello everyone,

I noticed that a few of you, like Conor and Alberto, mentioned issues with the <thorneyTreeLikelihood> configuration and the ThorneyBranchLengthLikelihoodDelegate in recent posts. I’m facing the same problem where BEAST reports that the <thorneyTreeLikelihood> element is incorrectly constructed and requires ThorneyBranchLengthLikelihoodDelegate.

Has anyone here managed to resolve this issue? If so, could you please share how you set up your XML to avoid these errors?

Additionally, if there’s a recommended workflow or a specific BEAST version where this setup is stable, that would be incredibly helpful to know. If anyone has an adjusted and functional XML for this type of analysis, I’d be very grateful for any guidance!

Thanks so much!

Alberto Aguayo

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Oct 22, 2024, 12:30:01 AM10/22/24
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Hello Vanise, I was available to running my Thorney-BEAST file using as template the xml file that is attached to this email (https://github.com/beast-dev/beast-mcmc/blob/master/examples/Benchmarks/thorney.xml).

Also I used the BEAST-version BEAST v1.10.5 pre-release of ThorneyTreeLikelihood v0.1.2 


Hope this helps you.

Best regards

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thorney (1).xml

JT McCrone

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Oct 24, 2024, 2:52:58 PM10/24/24
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Hello,

Sorry I missed these initial messages. 

There are some xml compatibility issues in using different in-progress versions of the method, but the template on the tutorial should work with pre-release also linked to in the tutorial. Please let me know if it doesn't! 

The next pre-release (soon!) should include beauti support for the thorney methods, which will also mark a final release xml api. 

Best,
JT
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