Issues with the Thorney Tree Likelihood Tutorial
Clara Malekshahi
Hello!
I have been trying to experiment with running BEAST starting with a tree to accommodate thousands of samples, as explained in this tutorial: Approaches for analyzing large phylogenetic datasets.
I first tried using the provided SG-thorney.template and beastgen to generate an XML file with my nwk tree. This give me the following error:
Exception in thread "main" java.lang. NullPointerException
I was able to use beastgen and the exact code provided in the tutorial linked above to recreate the example XML file with a SARS-CoV-2 tree, but beastgen would not work with my XML or my tree. To see if the issue was with my file, I then attempted to run the example XML file on BEAST (I tried with both BEAST X v10.5.0-beta5 and the beast-mcmc release referenced in a previous post that seemed to have the same problem). Unfortunately, neither worked, and I received errors like the following:
Error in input BEAST XML file, 1K_SARS-CoV-2_SG-thorney.xml:
The '«thorneyTreeLikelihoods' element, with id, 'treeLikelihood', is incorrectly constructed.
The following was expected:
Exactly one ELEMENT of type MutationBranchMap REQUIRED
I did try to run an XML file (with my tree) I generated manually, and I got the same error when running BEAST. I was hoping someone would either know which BEAST release is most likely to work or whether I am using an incorrect version of the example SARS-CoV-2 XML file. I am happy to post more information or to try running the example XML file again to double check. Any suggestions would be wonderful! Thank you so much!
Clara M.
Clara Malekshahi
Loading additional development parsers from development_parsers.properties, which is additional set of parsers only available for development version ...
Parsing XML file: 1K_SARS-CoV-2_SG-thorney.xml
File encoding: UTF8
Looking for plugins in /Volumes/BEAST v10.5.0/plugins
Looking for plugins in /Users/claramal/Desktop/Moncla_Lab/plugins
Overriding checkpointing settings in the provided XML file
Taxon list 'taxa' created with 1000 taxa.
most recent taxon date = 2020.5 years
Using node heights.
Creating the constrained tree model based on big fast tree model, 'treeModel'
taxon count = 1000
tree height = 0.4978826896494824
The gmrfSkyrideLikelihood has time aware smoothing
Creating a GMRF smoothed skyride model for multiple loci (SkyGrid)
Population sizes: 39
Feb 24, 2025 3:43:42 PM dr.app.beast.BeastMain <init>
SEVERE:
******
Error in input BEAST XML file, 1K_SARS-CoV-2_SG-thorney.xml:
The '<thorneyTreeLikelihood>' element, with id, 'treeLikelihood', is incorrectly constructed.
The following was expected:
Exactly one ELEMENT of type MutationBranchMap REQUIRED
******
Does anyone know where the issue is coming from here? Am I using the wrong BEAST version?
