Beauti crashes on alignment import

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Aron

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Oct 22, 2017, 3:31:04 AM10/22/17

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Hello,

I'm using Beast2.4.7, Java version 8.0152-b16. Every time I load a simple nexus format alignment Beauti crashes. I've also noticed that Beauti sometimes stalls on the loading screen after opening the software. I have to force quit java every time to get it to run.

Below is the error I get when I try to load an alignment. Any ideas? Thanks in advance!

Loading package BEAST v2.4.7

Loading package bModelTest v1.0.4

Loading package RBS v1.3.1

Loading package starbeast2 v0.13.5

Loading package SA v1.1.7

Loading package BEASTLabs v1.7.1

Loading package BEAST_CLASSIC v1.3.0

Loading package MM v1.0.5

Loading package STACEY v1.2.4

Loading package MODEL_SELECTION v1.3.4

Loading package substBMA v1.2.2

ch.randelshofer.quaqua.QuaquaLookAndFeel

Loading template /Users/aron/Desktop/BEAST2.4.7/templates/Standard.xml

Investigating /Users/aron/Library/Application Support/BEAST/2.4/MM

Processing /Users/aron/Library/Application Support/BEAST/2.4/MM/templates/morph-models.xml

Investigating /Users/aron/Library/Application Support/BEAST/2.4/BEAST

Processing /Users/aron/Library/Application Support/BEAST/2.4/BEAST/templates/ClockModels.xml

Processing /Users/aron/Library/Application Support/BEAST/2.4/BEAST/templates/Standard.xml

Processing /Users/aron/Library/Application Support/BEAST/2.4/BEAST/templates/ParametricDistributions.xml

Processing /Users/aron/Library/Application Support/BEAST/2.4/BEAST/templates/StarBeast.xml

Processing /Users/aron/Library/Application Support/BEAST/2.4/BEAST/templates/TreePriors.xml

Processing /Users/aron/Library/Application Support/BEAST/2.4/BEAST/templates/SubstModels.xml

Investigating lib

Investigating /Users/aron/Library/Application Support/BEAST/2.4/substBMA

Processing /Users/aron/Library/Application Support/BEAST/2.4/substBMA/templates/substBMA.xml

Processing /Users/aron/Library/Application Support/BEAST/2.4/substBMA/templates/wishartDistribution.xml

Investigating /Users/aron/Library/Application Support/BEAST/2.4/bModelTest

Processing /Users/aron/Library/Application Support/BEAST/2.4/bModelTest/templates/bModelTest.xml

Investigating .

Skipping /Users/aron/Desktop/BEAST2.4.7/./templates/ClockModels.xml since ClockModels.xml is already processed

Skipping /Users/aron/Desktop/BEAST2.4.7/./templates/Standard.xml since Standard.xml is already processed

Skipping /Users/aron/Desktop/BEAST2.4.7/./templates/ParametricDistributions.xml since ParametricDistributions.xml is already processed

Skipping /Users/aron/Desktop/BEAST2.4.7/./templates/StarBeast.xml since StarBeast.xml is already processed

Skipping /Users/aron/Desktop/BEAST2.4.7/./templates/TreePriors.xml since TreePriors.xml is already processed

Skipping /Users/aron/Desktop/BEAST2.4.7/./templates/SubstModels.xml since SubstModels.xml is already processed

Investigating /Users/aron/Library/Application Support/BEAST/2.4/RBS

Processing /Users/aron/Library/Application Support/BEAST/2.4/RBS/templates/RBS.xml

Processing /Users/aron/Library/Application Support/BEAST/2.4/RBS/templates/AutoPartition.xml

Investigating /Users/aron/Library/Application Support/BEAST/2.4/SA

Processing /Users/aron/Library/Application Support/BEAST/2.4/SA/templates/FBD.xml

Investigating /Users/aron/Library/Application Support/BEAST/2.4/BEASTLabs

Investigating /Users/aron/Library/Application Support/BEAST/2.4/MODEL_SELECTION

Investigating /Users/aron/Library/Application Support/BEAST/2.4/StarBEAST2

Processing /Users/aron/Library/Application Support/BEAST/2.4/StarBEAST2/templates/sbPopModels.xml

Cannot find merge point named sbPopModelTemplates from sbPopModels.xml in template. MergeWith ignored.

Processing /Users/aron/Library/Application Support/BEAST/2.4/StarBEAST2/templates/sbTreePriors.xml

Cannot find merge point named sbTreePriorTemplates from sbTreePriors.xml in template. MergeWith ignored.

Processing /Users/aron/Library/Application Support/BEAST/2.4/StarBEAST2/templates/sbClockModels.xml

Cannot find merge point named sbClockModelTemplates from sbClockModels.xml in template. MergeWith ignored.

Processing /Users/aron/Library/Application Support/BEAST/2.4/StarBEAST2/templates/SpeciesTreeUCED.xml

Processing /Users/aron/Library/Application Support/BEAST/2.4/StarBEAST2/templates/SpeciesTreeRLC.xml

Processing /Users/aron/Library/Application Support/BEAST/2.4/StarBEAST2/templates/sbSubstModels.xml

Cannot find merge point named sbSubstModelTemplates from sbSubstModels.xml in template. MergeWith ignored.

Processing /Users/aron/Library/Application Support/BEAST/2.4/StarBEAST2/templates/StarBeast2.xml

Processing /Users/aron/Library/Application Support/BEAST/2.4/StarBEAST2/templates/SpeciesTreeUCLN.xml

Investigating /Users/aron/Library/Application Support/BEAST/2.4/BEAST_CLASSIC

Processing /Users/aron/Library/Application Support/BEAST/2.4/BEAST_CLASSIC/templates/discrete-trait.xml

Processing /Users/aron/Library/Application Support/BEAST/2.4/BEAST_CLASSIC/templates/ClassicSubtseModels.xml

Investigating /Users/aron/Desktop/BEAST2.4.7

Skipping /Users/aron/Desktop/BEAST2.4.7/templates/ClockModels.xml since ClockModels.xml is already processed

Skipping /Users/aron/Desktop/BEAST2.4.7/templates/ParametricDistributions.xml since ParametricDistributions.xml is already processed

Skipping /Users/aron/Desktop/BEAST2.4.7/templates/StarBeast.xml since StarBeast.xml is already processed

Skipping /Users/aron/Desktop/BEAST2.4.7/templates/TreePriors.xml since TreePriors.xml is already processed

Skipping /Users/aron/Desktop/BEAST2.4.7/templates/SubstModels.xml since SubstModels.xml is already processed

Investigating /Users/aron/Library/Application Support/BEAST/2.4/STACEY

Processing /Users/aron/Library/Application Support/BEAST/2.4/STACEY/templates/STACEY.xml

Processing /Users/aron/Library/Application Support/BEAST/2.4/STACEY/templates/StarBeastWithSTACEYops.xml

map

beauticonfig

fragment

run

===============================================================================

Citations for this model:

Bouckaert RR, Heled J, Kuehnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA,

Rambaut A, Drummond AJ (2014) BEAST 2: A software platform for Bayesian

evolutionary analysis. PLoS Computational Biology 10(4): e1003537

===============================================================================

Warning: at least one operator required to run the MCMC properly, but none found.

template item TreeOperators is ignored

PARTITIONS0:

[[], [], []]

Could not find beastObject with id treeLikelihood.Species. Typo in template perhaps?

Validation message: At least one input of name 'xx' must be specified.

PARTITIONS0:

[[], [], []]

Alignment(null)

53 taxa

420 sites

241 patterns

plugin

beast.evolution.sitemodel.SiteModel.substModel: java.lang.ClassCastException: beast.evolution.alignment.FilteredAlignment cannot be cast to beast.evolution.substitutionmodel.SubstitutionModel

beast.evolution.sitemodel.SiteModel.substModel: java.lang.ClassCastException: beast.evolution.alignment.AlignmentFromTrait cannot be cast to beast.evolution.substitutionmodel.SubstitutionModel

beast.evolution.sitemodel.SiteModel.substModel: java.lang.ClassCastException: beast.evolution.alignment.AlignmentFromTraitMap cannot be cast to beast.evolution.substitutionmodel.SubstitutionModel

beast.evolution.sitemodel.SiteModel.substModel: java.lang.ClassCastException: beast.evolution.sitemodel.BEASTModelTestSiteModel cannot be cast to beast.evolution.substitutionmodel.SubstitutionModel

plugin

java.lang.IllegalArgumentException: Either input 'stateNumber' or 'datatype' needs to be specified

at beast.core.Input.validate(Unknown Source)

at beast.core.BEASTInterface.validateInputs(Unknown Source)

at beast.util.XMLParser.createObject(Unknown Source)

at beast.util.XMLParser.parseTemplate(Unknown Source)

at beast.app.beauti.BeautiSubTemplate.createSubNet(Unknown Source)

at beast.app.beauti.BeautiDoc.createInput(Unknown Source)

at beast.util.XMLParser.createBeastObject(Unknown Source)

at beast.util.XMLParser.createObject(Unknown Source)

at beast.util.XMLParser.parseTemplate(Unknown Source)

at beast.app.beauti.BeautiSubTemplate.createSubNet(Unknown Source)

at beast.app.beauti.BeautiDoc.addAlignmentWithSubnet(Unknown Source)

at beast.app.beauti.BeautiAlignmentProvider.addAlignments(Unknown Source)

at beast.app.beauti.BeautiAlignmentProvider.getAlignments(Unknown Source)

at beast.app.beauti.BeautiConfig.selectAlignments(Unknown Source)

at beast.app.beauti.AlignmentListInputEditor.addItem(Unknown Source)

at beast.app.beauti.AlignmentListInputEditor.access$000(Unknown Source)

at beast.app.beauti.AlignmentListInputEditor$1$1.run(Unknown Source)

at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)

at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)

at java.awt.EventQueue.access$500(EventQueue.java:97)

at java.awt.EventQueue$3.run(EventQueue.java:709)

at java.awt.EventQueue$3.run(EventQueue.java:703)

at java.security.AccessController.doPrivileged(Native Method)

at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)

at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)

at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)

at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)

at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)

at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)

at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)

at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

beast.util.XMLParserException:

Error 110 parsing the xml input file

validate and intialize error: Either input 'stateNumber' or 'datatype' needs to be specified

Error detected about here:

<beast>