java.lang.NullPointerException: Cannot invoke "Object.getClass()" because "<local3>" is null

[genesandbones]

Hello,
I apologize that this issue has been listed before but I could not find a resolution that was useful for my scenario.
I was trying to help my partner troubleshoot her problems with running PathSampler and figured I would try on my computer with a completely fresh install of Beast and MODEL_SELECTION, worried that her multiple versions of Beast was causing java issues.

Alas, even on my completely new install (this computer has never had BEAST on it) I still get the same object class error and I'm not sure how to fix it.
All I did was run the example model file and set a new folder tmp directory. No other params were changed, just testing the new install out.

Here is my complete output:
java.lang.NoSuchMethodException: sa.beauti.SampledNodeDataWalkerInputEditor.(beastfx.app.inputeditor.BeautiDoc)
Exception in thread "JavaFX Application Thread" java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0
at beastfx.app.util.FXUtils.getLoadFile(Unknown Source)
at beastfx.app.inputeditor.FileInputEditor.lambda$init$0(Unknown Source)
at javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
at javafx.base/javafx.event.Event.fireEvent(Unknown Source)
at javafx.graphics/javafx.scene.Node.fireEvent(Unknown Source)
at javafx.controls/javafx.scene.control.Button.fire(Unknown Source)
at javafx.controls/com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(Unknown Source)
at javafx.controls/com.sun.javafx.scene.control.inputmap.InputMap.handle(Unknown Source)
at javafx.base/com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
at javafx.base/javafx.event.Event.fireEvent(Unknown Source)
at javafx.graphics/javafx.scene.Scene$MouseHandler.process(Unknown Source)
at javafx.graphics/javafx.scene.Scene.processMouseEvent(Unknown Source)
at javafx.graphics/javafx.scene.Scene$ScenePeerListener.mouseEvent(Unknown Source)
at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
at java.base/java.security.AccessController.doPrivileged(Unknown Source)
at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(Unknown Source)
at javafx.graphics/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(Unknown Source)
at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(Unknown Source)
at javafx.graphics/com.sun.glass.ui.View.handleMouseEvent(Unknown Source)
at javafx.graphics/com.sun.glass.ui.View.notifyMouse(Unknown Source)
at javafx.graphics/com.sun.glass.ui.win.WinApplication._enterNestedEventLoopImpl(Native Method)
at javafx.graphics/com.sun.glass.ui.win.WinApplication._enterNestedEventLoop(Unknown Source)
at javafx.graphics/com.sun.glass.ui.Application.enterNestedEventLoop(Unknown Source)
at javafx.graphics/com.sun.glass.ui.EventLoop.enter(Unknown Source)
at javafx.graphics/com.sun.javafx.tk.quantum.QuantumToolkit.enterNestedEventLoop(Unknown Source)
at javafx.graphics/javafx.stage.Stage.showAndWait(Unknown Source)
at javafx.controls/javafx.scene.control.HeavyweightDialog.showAndWait(Unknown Source)
at javafx.controls/javafx.scene.control.Dialog.showAndWait(Unknown Source)
at beastfx.app.tools.Application.createDialog(Unknown Source)
at beastfx.app.util.Console$2.run(Unknown Source)
at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runLater$10(Unknown Source)
at java.base/java.security.AccessController.doPrivileged(Unknown Source)
at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runLater$11(Unknown Source)
at javafx.graphics/com.sun.glass.ui.InvokeLaterDispatcher$Future.run(Unknown Source)
at javafx.graphics/com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
at javafx.graphics/com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
java.lang.NullPointerException: Cannot invoke "Object.getClass()" because "" is null
at modelselection.inference.PathSampler.run(Unknown Source)
at beastfx.app.tools.Application.createDialog(Unknown Source)
at beastfx.app.util.Console$2.run(Unknown Source)
at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runLater$10(Unknown Source)
at java.base/java.security.AccessController.doPrivileged(Unknown Source)
at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runLater$11(Unknown Source)
at javafx.graphics/com.sun.glass.ui.InvokeLaterDispatcher$Future.run(Unknown Source)
at javafx.graphics/com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
at javafx.graphics/com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
Path Sampler done in 0 seconds. Close window to finish application.

Any tips on how to proceed to fix the getclass error on this fresh install would be greatly appreciated :)

[genesandbones]

Hello,

Ok I have figured out the above, now I'm having an issue where the path isn't correct running PathSampler. The output shows no "" in the paths which is probably making it fail. Here is example: C:\Users\Tre\OneDrive\Documents\20251109_BEASTTEST\step0>"C:UsersTreBEASTBEAST.v2.7.7.WindowsBEAST./jre/bin/java.exe" -cp "C:/Users/Tre/BEAST/BEAST.v2.7.7.Windows/BEAST/./lib/launcher.jar" beast.pkgmgmt.launcher.BeastLauncher -overwrite -java -seed 18818793 beast.xml
The system cannot find the path specified.

Is the path something I need to manually edit or why is it removing the directories in the path?

[rbouckaert]

Not sure what is happening, but it tries to replace $(java) in the XML with where it thinks java.exe is. A quick fix may be to edit the XML and replace $(java) by hand with
C:/Users/Tre/BEAST/BEAST.v2.7.7.Windows/BEAST./jre/bin/java.exe and see if the problem persists.

[genesandbones]

I don't see where the java assignment is in the xml either. Where should that be? Even the tests pathsampler files don't have a java path assignment in the xml

[rbouckaert]

In examples/NormalTestPS-2.xm, just after the run element, it contains the script, like so:

<run spec='beast.inference.PathSampler' chainLength="500000" alpha='0.3' rootdir='/tmp/step' burnInPercentage='50' preBurnin="50000" deleteOldLogs='true' nrOfSteps='100'>
cd $(dir)
$(java) -cp $(java.class.path) beast.pkgmgmt.launcher.BeastLauncher $(resume/overwrite) -seed $(seed) beast.xml

Here $(java) gets replaced (unsuccessfully on your computer), but if you edit so it looks like this:

<run spec='beast.inference.PathSampler' chainLength="500000" alpha='0.3' rootdir='/tmp/step' burnInPercentage='50' preBurnin="50000" deleteOldLogs='true' nrOfSteps='100'>
cd $(dir)
C:/Users/Tre/BEAST/BEAST.v2.7.7.Windows/BEAST./jre/bin/java.ex -cp $(java.class.path) beast.pkgmgmt.launcher.BeastLauncher $(resume/overwrite) -seed $(seed) beast.xml

it may pick up the correct java executable. Let me know if this fixes the problem.

[genesandbones]

Hello, Ok that seemed to have helped with the pathing but now I'm getting this error, even running PathSampler on NormalTestPs-2 Exception in thread "JavaFX Application Thread" java.lang.IllegalArgumentException: The model in C:\Users\Tre\BEAST\2.7\MODEL_SELECTION\examples\normalTestPS-2.xml does not appear to be an MCMC analysis.

…

On Sun, Nov 23, 2025 at 3:19 PM Remco Bouckaert ***@***.***> wrote: *rbouckaert* left a comment (CompEvol/beast2#1208) <#1208 (comment)> In examples/NormalTestPS-2.xm <https://github.com/BEAST2-Dev/model-selection/blob/master/examples/normalTestPS-2.xml>, just after the run element, it contains the script, like so: <run spec='beast.inference.PathSampler' chainLength="500000" alpha='0.3' rootdir='/tmp/step' burnInPercentage='50' preBurnin="50000" deleteOldLogs='true' nrOfSteps='100'> cd $(dir) $(java) -cp $(java.class.path) beast.pkgmgmt.launcher.BeastLauncher $(resume/overwrite) -seed $(seed) beast.xml Here $(java) gets replaced (unsuccessfully on your computer), but if you edit so it looks like this: <run spec='beast.inference.PathSampler' chainLength="500000" alpha='0.3' rootdir='/tmp/step' burnInPercentage='50' preBurnin="50000" deleteOldLogs='true' nrOfSteps='100'> cd $(dir) C:/Users/Tre/BEAST/BEAST.v2.7.7.Windows/BEAST./jre/bin/java.ex -cp $(java.class.path) beast.pkgmgmt.launcher.BeastLauncher $(resume/overwrite) -seed $(seed) beast.xml it may pick up the correct java executable. Let me know if this fixes the problem. — Reply to this email directly, view it on GitHub <#1208 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJDMW5MYGCHVL6QPFESFCVD36IXIRAVCNFSM6AAAAACLTAHP46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTKNRYGM4TMOBTHA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Thanks, Tre Blohm, PhD, MDT(AMT)

[rbouckaert]

NormalTestPS-2.xml is supposed to be run with BEAST, not with the PathSampler app.

If you have an MCMC analysis XML prepared with BEAUti, perhaps the best way is to run the PathSampler app with that XML as model, but set the do not run flag, so it only creates BEAST XML files + a script to run these XMLs. In the script, replace the corrupted path to java with the correct path (C:/Users/Tre/BEAST/BEAST.v2.7.7.Windows/BEAST./jre/bin/java.exe), then run the script. Hope this helps.

[genesandbones]

Hello, Ok perhaps I need some direction to running pathsampler. The tutorials and instructions on beast are unclear as to what processing needs to happen to the xml file before hand and whether with the newer beast version, if we have to still do the manual xml file edit to make it work. Would you be able to walk me through how to run pathsampler? I tried the above and it didn't generate any script file. Where would that file be generated? It doesn't appear to go to the root dir I give it. Additionally, trying to run the example files fails with: java.io.FileNotFoundException: C:\tmp\step\step9\beast.xml.state (The system cannot find the file specified).

…

On Sun, Nov 23, 2025 at 4:51 PM Remco Bouckaert ***@***.***> wrote: *rbouckaert* left a comment (CompEvol/beast2#1208) <#1208 (comment)> NormalTestPS-2.xml is supposed to be run with BEAST, not with the PathSampler app. If you have an MCMC analysis XML prepared with BEAUti, perhaps the best way is to run the PathSampler app with that XML as model, but set the do not run flag, so it only creates BEAST XML files + a script to run these XMLs. In the script, replace the corrupted path to java with the correct path (C:/Users/Tre/BEAST/BEAST.v2.7.7.Windows/BEAST./jre/bin/java.exe), then run the script. Hope this helps. — Reply to this email directly, view it on GitHub <#1208 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJDMW5M74ZWYBMC4524NZZD36JCABAVCNFSM6AAAAACLTAHP46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTKNRYGQ3TMNZYGI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Thanks, Tre Blohm, PhD, MDT(AMT)