Can't import alignment in Beauti when MM is installed

[3r1d]

Hi,

I face an error when I try to import alignments in BEAUti.

I see "getFrequencies() is null" message in the log and no partition get created (I tried with different nexus files, same issue each time).

I am using versions below:

Beast2
commit d5cb7f1 (HEAD)

Beauti
commit e59fe8c6d423013fa5a004ee5030bcde6f193ab2 (HEAD)

MM (morph-models)
1.2.1

Notes:

• If I don't load MM package, I can import alignments.

• If I comment the block below in SiteModelInterface.java, I can import alignments.

// sanity check: make sure the number of states from dataType matches that of the substitution model
if (m_dataType != null) {
    int nrOfStatesInData = m_dataType.getStateCount();
    if (nrOfStatesInData >= 0) {
        int nrOfFrequencies = substModelInput.get().getFrequencies().length;
        if (nrOfStatesInData != nrOfFrequencies) {
            throw new IllegalArgumentException("Number of states in data (" + nrOfStatesInData + ") differs from number of frequencies (" + nrOfFrequencies +")");
        }
    }
}

Exception details:

validate and intialize error: initAndValidate() failed! Cannot read the array length because the return value of "beast.base.evolution.substitutionmodel.SubstitutionModel.getFrequencies()" is null

Error detected about here:
  <beast>
      <plugin id='treeLikelihood.penguins_dna' spec='ThreadedTreeLikelihood'>

	at beast.base.parser.XMLParser.initBEASTObjects(XMLParser.java:525)
	at beast.base.parser.XMLParser.parseTemplate(XMLParser.java:508)
	at beastfx.app.inputeditor.BeautiSubTemplate.createSubNet(BeautiSubTemplate.java:386)
	at beastfx.app.inputeditor.BeautiSubTemplate.createSubNet(BeautiSubTemplate.java:352)
	at beastfx.app.inputeditor.BeautiDoc.addAlignmentWithSubnet(BeautiDoc.java:1637)
	at beastfx.app.inputeditor.BeautiAlignmentProvider.addAlignments(BeautiAlignmentProvider.java:231)
	at beastfx.app.inputeditor.BeautiAlignmentProvider.getAlignments(BeautiAlignmentProvider.java:187)
	at beastfx.app.inputeditor.BeautiAlignmentProvider.getAlignments(BeautiAlignmentProvider.java:108)
	at beastfx.app.beauti.BeautiTabPane$2.actionPerformed(BeautiTabPane.java:839)
	at beastfx.app.inputeditor.MyAction.lambda$0(MyAction.java:90)
	at javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
	at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:232)
	at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:189)
	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
	at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
	at javafx.base/javafx.event.Event.fireEvent(Event.java:199)
	at javafx.controls/javafx.scene.control.MenuItem.fire(MenuItem.java:459)
	at javafx.controls/com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.doSelect(ContextMenuContent.java:1415)
	at javafx.controls/com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.lambda$createChildren$12(ContextMenuContent.java:1368)
	at javafx.base/com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247)
	at javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
	at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:232)
	at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:189)
	at javafx.base/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
	at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
	at javafx.base/javafx.event.Event.fireEvent(Event.java:199)
	at javafx.graphics/javafx.scene.Scene$MouseHandler.process(Scene.java:3985)
	at javafx.graphics/javafx.scene.Scene.processMouseEvent(Scene.java:1891)
	at javafx.graphics/javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2709)
	at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:411)
	at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:301)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:399)
	at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:450)
	at javafx.graphics/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:430)
	at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:449)
	at javafx.graphics/com.sun.glass.ui.View.handleMouseEvent(View.java:551)
	at javafx.graphics/com.sun.glass.ui.View.notifyMouse(View.java:937)
	at javafx.graphics/com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
	at javafx.graphics/com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$10(GtkApplication.java:266)
	at java.base/java.lang.Thread.run(Thread.java:840)

beast.base.evolution.sitemodel.SiteModel.substModel: java.lang.ClassCastException: class beast.base.evolution.alignment.FilteredAlignment cannot be cast to class beast.base.evolution.substitutionmodel.SubstitutionModel (beast.base.evolution.alignment.FilteredAlignment and beast.base.evolution.substitutionmodel.SubstitutionModel are in unnamed module of loader 'app')
beast.base.evolution.sitemodel.SiteModel.substModel: java.lang.ClassCastException: class beast.base.evolution.sitemodel.SiteModel cannot be cast to class beast.base.evolution.substitutionmodel.SubstitutionModel (beast.base.evolution.sitemodel.SiteModel and beast.base.evolution.substitutionmodel.SubstitutionModel are in unnamed module of loader 'app')

[rbouckaert]

With the released version of BEAST v2.7.8 and MM v1.2.1, I can do

• File/Import Alignment and select examples/nexus/penguins_dna.nex from the morph models package, then
• File/Add Morphological Data and select examples/nexus/penguins_morph.nex from the morph models package, click the pop-up dialog.
  This does not result in any error, and shows 1 dna and 6 morph partitions in the partitions panel.
  Any idea what could have been different in your situation?

[3r1d]

One reason could be that you are on the v2.7.8 tag (a40b83d) as the commit preventing the alignment import is between the v2.7.8 tag and the HEAD (ff4d7ec - Tue Sep 2 10:14:45 2025).

[3r1d]

One other thing that may explain the difference is that I am running Beauti from Eclipse.

The command line Eclipse use is:

/home/foo/opt/zulu17.64.17-ca-fx-jdk17.0.18-linux_x64/bin/java -Dbeast.debug=true -Dfile.encoding=UTF-8 -Dstdout.encoding=UTF-8 -Dstderr.encoding=UTF-8 -classpath /home/f
oo/workspace/BeastFX/bin:/home/foo/workspace/BeastFX/locallib/assertj-core-3.20.2.jar:/home/foo/workspace/BeastFX/locallib/jam.jar:/home/foo/workspace/BeastFX/locallib/testfx.jar:/home/foo/workspace/beast2/bin:/home/foo/workspace/beast2/lib/antlr-runtime-4.10.1.jar:/home/foo/workspace/beast2/lib/beagle.jar:/home/foo/workspace/beast2/lib/bundler/jarbundler-core-3.3.0.jar:/home/foo/workspace/beast2/lib/colt.jar:/home/foo/workspace/beast2/lib/commons-math3-3.6.1.jar:/home/foo/workspace/beast2/lib/junit/junit-platform-console-standalone-1.8.2.jar beastfx.app.beauti.Beauti


When I build a release with Ant (then install it and run Beauti with: $ /opt/beast/bin/beauti), I can import alignment.

[3r1d]

With steps below, it is possible to reproduce the error without Eclipse

1. Install MM using packagemanager (GUI mode)

git clone https://github.com/CompEvol/beast2
git clone https://github.com/CompEvol/BeastFX
rm -rf ~/.beast # start from scratch
cd BeastFX

$ /opt/zulu17.64.17-ca-fx-jdk17.0.18-linux_x64/bin/java \
-Dbeast.debug=true -Dfile.encoding=UTF-8 -Dstdout.encoding=UTF-8 -Dstderr.encoding=UTF-8 \
-classpath /workspace/BeastFX/build:\
/workspace/BeastFX/locallib/assertj-core-3.20.2.jar:/workspace/BeastFX/locallib/jam.jar:/workspace/BeastFX/locallib/testfx.jar:\
/workspace/beast2/build:\
/workspace/beast2/lib/antlr-runtime-4.10.1.jar:/workspace/beast2/lib/beagle.jar:/workspace/beast2/lib/bundler/jarbundler-core-3.3.0.jar:\
/workspace/beast2/lib/colt.jar:/workspace/beast2/lib/commons-math3-3.6.1.jar:/workspace/beast2/lib/junit/junit-platform-console-standalone-1.8.2.jar \
beastfx.app.beauti.Beauti

In Beauti, do

• click File=>"Manage packages"
• select MM pkg
• click "Install"
• close Beauti

After that, we have the following in ~/.beast

root@94198c18e397:/workspace# ls -1 /root/.beast/2.7/
MM
beauti.properties

2. Then we try to import an alignment

cd BeastFX
/opt/zulu17.64.17-ca-fx-jdk17.0.18-linux_x64/bin/java \
-Dbeast.debug=true -Dfile.encoding=UTF-8 -Dstdout.encoding=UTF-8 -Dstderr.encoding=UTF-8 \
-classpath /workspace/BeastFX/build:\
/workspace/BeastFX/locallib/assertj-core-3.20.2.jar:/workspace/BeastFX/locallib/jam.jar:/workspace/BeastFX/locallib/testfx.jar:\
/workspace/beast2/build:\
/workspace/beast2/lib/antlr-runtime-4.10.1.jar:/workspace/beast2/lib/beagle.jar:/workspace/beast2/lib/bundler/jarbundler-core-3.3.0.jar:\
/workspace/beast2/lib/colt.jar:/workspace/beast2/lib/commons-math3-3.6.1.jar:/workspace/beast2/lib/junit/junit-platform-console-standalone-1.8.2.jar \
beastfx.app.beauti.Beauti -nex /workspace/morph-models/examples/nexus/penguins_dna.nex

It fails with the "getFrequencies() is null" message.

To be noted that when we install MM using packagemanager in CLI mode, we don't have the error anymore.

rm -rf ~/.beast # start from scratch
cd beast2 && java -cp build beast.pkgmgmt.PackageManager -add MM

This is because the behaviour is not exactly the same depending on using packagemanager in CLI mode or in GUI mode.

In GUI mode, installing MM package results with just the MM package installed in ~/.beast.

while in CLI mode, installing MM package results with the MM package and the BEAST.app package installed in ~/.beast