Ancestral state reconstruction in *BEAST (ambiguities)

Luiz JQ

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Nov 16, 2017, 2:01:54 PM11/16/17

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Dear all,

I’ve been trying to reconstruct ancestral states of a given trait using *Beast (v 2.4.7).

When I don’t set ambiguities in the XML file, it runs smoothly. However, when I include them, I always get an error message. I’ve trying to find an effective solution from the beast-users’ discussion, but I can’t succeed. That’s why I’m asking this here. Maybe someone could give me a little help.

Basically, I included the flag useAmbiguities=”true”, and added a new code.

Below, you can see the part of the XML file where the modifications have been done, and then the error message.

Many thanks in advance.

<data

id="area"

spec="AlignmentFromTrait">

<traitSet id="traitSet.area" spec="beast.evolution.tree.TraitSet" taxa="@taxonsuperset" traitname="discrete">sp1=ori,

sp2=aml_mad,

sp3=gui,

sp4=mar,

sp5=aml,

sp6=mad,

sp7=aml</traitSet>

Sample posterior ESS(posterior) likelihood prior

Fatal exception: null

java.lang.NullPointerException

at java.lang.System.arraycopy(Native Method)

at beast.evolution.likelihood.BeerLikelihoodCore.getNodeStates(Unknown Source)

at beast.evolution.likelihood.AncestralStateTreeLikelihood.traverseSample(Unknown Source)

at beast.evolution.likelihood.AncestralStateTreeLikelihood.redrawAncestralStates(Unknown Source)

at beast.evolution.likelihood.AncestralStateTreeLikelihood.getStatesForNode(Unknown Source)

at beast.evolution.likelihood.AncestralStateTreeLikelihood$1.getTraitString(Unknown Source)

at beast.evolution.tree.TreeWithTraitLogger.toNewick(Unknown Source)

at beast.evolution.tree.TreeWithTraitLogger.log(Unknown Source)

at beast.core.Logger.log(Unknown Source)

at beast.core.MCMC.log(Unknown Source)

at beast.core.MCMC.propagateState(Unknown Source)

at beast.core.MCMC.doLoop(Unknown Source)

at beast.core.MCMC.run(Unknown Source)

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

at beast.app.beastapp.BeastMain.<init>(Unknown Source)

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

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

Fatal exception: null

Luiz JQ

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Nov 20, 2017, 12:02:50 PM11/20/17

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I tried to run the same xml file, but without the flag useAmbiguities="true". It ran. However, the analysis is estimating the most likely distribution area for the the sp2 between the two I gave with my ambiguous code (sp2=aml_mad), instead of considering a priori both areas as true distribution areas. So, I suppose that somehow I must include the flag. Am I wright?

Remco Bouckaert

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Nov 27, 2017, 3:35:02 AM11/27/17

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Hi Luiz,

Thanks for the XML, that was helpful in finding the problem. There was a bug in the ancestral state reconstruction code when not using BEAGLE. I think I fixed it now, and when you update to BEAST_CLASSIC v1.3.1 your file should run.

However, given you have just 7 taxa in the species tree from 5 locations, and one of the tips is ambiguous, it will be very hard to say something about ancestral states based on this information alone. You might consider reducing the number of locations, or use a diffusions based geographical reconstruction instead (if a random walk model is appropriate for your species).

Cheers,

Remco

On 21/11/2017, at 6:02 AM, Luiz JQ <ljq...@gmail.com> wrote:

I tried to run the same xml file, but without the flag useAmbiguities="true". It ran. However, the analysis is estimating the most likely distribution area for the the sp2 between the two I gave with my ambiguous code (sp2=aml_mad), instead of considering a priori both areas as true distribution areas. So, I suppose that somehow I must include the flag. Am I wright?

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Luiz JQ

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Nov 27, 2017, 5:40:46 AM11/27/17

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Many thanks, Remco!

I updated beast_classic and it ran.

Thank you for the advice as well. In fact, this is just a pilot analysis to make sure that it runs smoothly before running with the complete dataset. I have ~100 taxa distributed among ~300 samples. I'll see if it's enough for a good reconstruction soon.

Have a nice week

Luiz

zany...@gmail.com

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Apr 29, 2024, 5:44:22 AM4/29/24

to beast-users

Hello Dr Bouckaert,

I have a similar problem with multiple discrete states not being recognized. I am using BEAST_CLASSIC 1.5.0 with Beagle 3.1.0 and have included and excluded useAmbiguities="true", but either way I get an error in the attached screen output

Could I please have some help setting up the discrete states?

Best,

Zaynab

BEAST v2.6.7, 2002-2022
Bayesian Evolutionary Analysis Sampling Trees
Designed and developed by
Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard

Centre for Computational Evolution
University of Auckland
r.bou...@auckland.ac.nz
ale...@cs.auckland.ac.nz

Institute of Evolutionary Biology
University of Edinburgh
a.ra...@ed.ac.uk

David Geffen School of Medicine
University of California, Los Angeles
msuc...@ucla.edu

Downloads, Help & Resources:
http://beast2.org/

Source code distributed under the GNU Lesser General Public License:
http://github.com/CompEvol/beast2

BEAST developers:
Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled,
Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li,
Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel,
Oliver Pybus, Tim Vaughan, Chieh-Hsi Wu, Walter Xie

Thanks to:
Roald Forsberg, Beth Shapiro and Korbinian Strimmer

Random number seed: 1714383499870

Alignment(Disparago_ericoides_locus-17_aligned_taper)
135 taxa
1265 sites
491 patterns

Starting frequencies: [0.2795511809463119, 0.17589763818718127, 0.21128346477161758, 0.33326771609540995]
Using BEAGLE version: 3.1.0 resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU
Amphiglossa_celans_S1.1_SK = SK (NaN)
Amphiglossa_celans_S1_SK = SK (NaN)
Amphiglossa_foliosa_S3.1_SK = SK (NaN)
Amphiglossa_foliosa_S3_SK = SK (NaN)
Amphiglossa_grisea_S4.1_NW = NW (NaN)
Amphiglossa_grisea_S4_NW = NW (NaN)
Amphiglossa_tomentosa_S11.1_NW_KM = NW_KM (NaN)
Amphiglossa_tomentosa_S11_NW_KM = NW_KM (NaN)
Amphiglossa_tomentosa_S12.1_NW_KM = NW_KM (NaN)
Amphiglossa_tomentosa_S12_NW_KM = NW_KM (NaN)
125 more...

Error 110 parsing the xml input file

validate and intialize error: Could not find code NW_KM in codemap

Error detected about here:
<beast>
<run id='mcmc' spec='MCMC'>
<distribution id='posterior' spec='util.CompoundDistribution'>
<distribution id='likelihood' spec='util.CompoundDistribution'>
<distribution id='traitedtreeLikelihood.Lojava.lang.IllegalArgumentException: Could not find code NW_KM in codemap
at beast.evolution.datatype.DataType$Base.stringToEncoding(Unknown Source)
at beast.evolution.datatype.DataType$Base.string2state(Unknown Source)
at beast.evolution.alignment.AlignmentFromTrait.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)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at beast.app.beastapp.BeastLauncher.run(Unknown Source)
at beast.app.beastapp.BeastLauncher.main(Unknown Source)
cation' spec='AncestralStateTreeLikelihood'>
<data id='Location' spec='AlignmentFromTrait'>

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