BEAST2+MultiTypeTree: Internal node only has a single child

[Ruoyun Hui]

Hi all,

I'm running BEAST v 2.2.0 with the package MultiTypeTree on a two-deme model. The BEAST run finished smoothly, but when I launch TreeAnnotator on the .trees file, I get the following screen output:

Reading trees (bar assumes 10,000 trees)...

0              25             50             75            100

|--------------|--------------|--------------|--------------|

May 14, 2015 7:08:15 PM dr.evolution.io.NexusImporter readInternalNode

WARNING: Internal node only has a single child!

May 14, 2015 7:08:15 PM dr.evolution.io.NexusImporter readInternalNode

WARNING: Internal node only has a single child!

May 14, 2015 7:08:15 PM dr.evolution.io.NexusImporter readInternalNode

WARNING: Internal node only has a single child!

....

The warnings go on forever. Indeed something seems wrong with the recorded trees, as I cannot visualize them in FigTree either.

I wonder what might cause BEAST to generate such node with one child, and what I can do to avoid the problem?

Thank you!

[Tim Vaughan]

Hi Ruoyun,

MultiTypeTree produces trees that are fully annotated with a migration
history. Migration events are represented by single child nodes. You
should definitely be able to visualize them using either FigTree or
IcyTree (http://tgvaughan.github.io/icytree). What errors are you
seeing from FigTree?

TreeAnnotator can't, as far as I know, handle summarize these kinds of
trees. However, if you upgrade to the latest versions of BEAST
(2.2.1) and MultiTypeTree (5.3.0) and then reassemble your analysis in
BEAUti, the analysis will produce an additional tree file with the
extension .typedNode.trees. This file contains trees annotated with
locations only at coalescent nodes and can be analyzed as per usual
using TreeAnnotator.

Hope this helps!

Tim

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[Ruoyun Hui]

Hi Tim,

Thank you so much for the help! The updated version solves the problem :)

And yes, IcyTree (great tool!) shows my previous trees without problem, but FigTree reports a stack overflow error in java. 

Best,

Ruoyun

[qianku...@gmail.com]

HI everyone,
 
Recently,I am running the BEAST to use the MultitypeTree package to get the
three type tree on a six-demo model.The BEAST run finished smoothly,and I
get the three type tree with 6.map.trees,6.trees and 6.typedNode.tree as the
Beginner's Tutorial said.But I can only load the typedNode.tree in the
IcyTree website and all the three trees can't been visualized in the
Figtree.I want to get the summary tree by the TreeAnnotator to use the
typedNode.tree as the tutorial said,but I get the wrong message like this: 
 
TreeAnnotator v2.3.0, 2002-2015
 
MCMC Output analysis
 
by
 
Andrew Rambaut and Alexei J. Drummond
 
 
 
Institute of Evolutionary Biology
 
University of Edinburgh
 
a.ra...@ed.ac.uk
 
 
 
Department of Computer Science
 
University of Auckland
 
ale...@cs.auckland.ac.nz

 
 
 
 
 
0 25 50 75 100
 
|--------------|--------------|--------------|--------------|
 

*************************************************************
 
java.lang.NullPointerException
 
at beast.evolution.tree.Tree.setRoot(Unknown Source)
 
at beast.evolution.tree.Tree.<init>(Unknown Source)
 
at beast.app.treeannotator.TreeAnnotator.<init>(Unknown Source)
 
at beast.app.treeannotator.TreeAnnotator.main(Unknown Source)
 
at beast.app.treeannotator.TreeAnnotatorLauncher.main(Unknown
Source)
 
Error Parsing Input Tree: null
 
Finished - Quit program to exit.
 
This typedNode.tree is complete and I don't know what is the wrong with
it.Can you tell me how to solve these problem.
 
Thanks a lot!
 
Best,
 
Qiankun Zhang
 

在 2015年5月15日星期五 UTC+8上午1:21:09，Ruoyun Hui写道：

[Tim Vaughan]

Hi Qiankun,

I I'm sorry to hear about this problem.  In case you were worried, I did receive the emails you sent me last night but I haven't been able to look at this yet.  I'll try to figure out what's going on when I get into the office tomorrow morning (New Zealand time).

All the best,

Tim

--

[Tim Vaughan]

Hi again Qiankun,

1. What exactly do you mean by a "three type tree on a six deme model"?

2. It's very peculiar that you can't view the MAP tree file or the fully typed tree file (6.trees) in IcyTree.  What happens when you try to load these files?

3. The TreeAnnotator issue looks like it could be the result of a malformed tree file.  Is there any chance you might be able to send me a (zipped) copy of this file?

Cheers,

Tim

--

[yanha...@gmail.com]

在 2015年5月14日星期四 UTC-7上午10:21:09，Ruoyun Hui写道：