v2.5.2 - Starting tree: Error 110 parsing the xml input file

[RNP]

I am trying to date a tree using a phylogeny from a previous Bayes run. To do this I know that I need to add the previous tree as a starting tree, then remove operators that act on the topology.  In addition I want to add a prior to the tree height.  The XML file is attached. When I run the file in beast I get the following:

File: b252_fixed_topo_rU25.xml seed: 1559923069353 threads: 1

Random number seed: 1559923069353

Alignment(PmanicTrunk)

  502 taxa

  1143 sites

  569 patterns

Error 110 parsing the xml input file

validate and intialize error: null

Error detected about here:

  <beast>

      <run id='mcmc' spec='MCMC'>

          <init id='NewickTree.t:PmanicTrunk' spec='beast.util.TreeParser'>

java.lang.NullPointerException

at beast.evolution.tree.Tree.initAndValidate(Unknown Source)

at beast.util.TreeParser.initAndValidate(Unknown Source)

at beast.util.XMLParser.initBEASTObjects(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)

My reading of the error is that it is an XML formatting issue caused by the addition of my starting tree.  At this point I have tried adding the starting tree using documentation from https://justinbagley.rbind.io/2014/02/17/got-starting-tree-add-beast2-xml-file-make-work/, https://www.beast2.org/2014/07/28/all-about-starting-trees, and https://www.beast2.org/fix-starting-tree/ and directly with BEAUTi (2.5.2) and have the same error.

The file runs when I comment out the <init id... block so I know the error is in there.  I have examined and exported the newick tree from figtree.

I am using BEAST and BEAUTi (v2.5.2) and am working on a windows machine.  I have been trouble shooting this problem for a few days now and am at the end or my rope.  I am hoping fresh eyes can help. 

Thanks in advance.

[Remco Bouckaert]

Hi Neal, 

It looks like there is a sequence for taxon Gam.MSB53348.MN, but that taxon is not in the starting tree. There is currently no check for that situation, so you get this obscure NullPointerException (but I logged an issue #859 to fix this). Adding Gam.MSB53348.MN to the tree (and possibly other missing taxa, I only spotted this one) should fix the problem.

Cheers,

Remco

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<b252_fixed_topo_rU25.xml>