Beauti doesnt open

[Dustin Wood]

Hi there,

I just downloaded the BEAST 2.7.0 for mac running macOS Monterey 12.6. 

I can't get BEAUti to open, it just bounces (a flash) and then its gone. Has anyone else experienced this or have a known solution? I can't seem to find anything on group. 

Thanks!

[Dustin Wood]

More detail to help troubleshoot the issue

1) This is NOT due to the Gate Keeper issue where you have to set the System Preferences Security to allow apps from anywhere. I already have that set and I still get the issue. 

2) The mac JAVA should be fine but I checked that:

java version "1.8.0_333"

Java(TM) SE Runtime Environment (build 1.8.0_333-b02)

Java HotSpot(TM) 64-Bit Server VM (build 25.333-b02, mixed mode)

[higg...@gmail.com]

Hi Dustin,

Can you start BEAUti through a terminal? If not, what error message do you get when you use this in a terminal:

/Applications/BEAST\ 2.7.0/bin/beauti

(note the backslash before the space) assuming you have BEAST installed in /Applications/BEAST 2.7.0?

Cheers,

Remco

PS A java 17 runtime is included in the distribution, so it is no longer necessary to have a jdk installed.

[Dustin Wood]

Hi Remco

I tried running it through the terminal and it did run, but it's running v1.10.4, which doesn't seem correct. This is an old version, no?

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[Dustin Wood]

Here's the line I used in the terminal: dawood$ cd Applications/BEAST\ 2.7.0/bin/

and then I typed  beauti 

[higg...@gmail.com]

Can you try ./beauti (that is add ./ before beauti) so it won't look in your path but in the specific directory?

[Dustin Wood]

Ok, that did not work. I get this:

dawood$ ./beauti
Loading package BICEPS v1.1.0 speedemon v1.1.0 starbeast3 v1.1.2 BEAST.base v2.7.0 BEASTLabs v2.0.0 BEAST.app v2.7.0 snapper v1.1.0 ORC v1.1.0 SNAPP v1.6.1    
ch.randelshofer.quaqua.QuaquaLookAndFeel
Loading template /Users/dawood/Library/Application Support/BEAST/2.7/BEAST.app/fxtemplates/Standard.xml
Investigating
Investigating /Users/dawood/Library/Application Support/BEAST/2.7/SNAPP
Processing /Users/dawood/Library/Application Support/BEAST/2.7/SNAPP/fxtemplates/SNAPP.xml
Investigating /Users/dawood/Library/Application Support/BEAST/2.7/speedemon
Processing /Users/dawood/Library/Application Support/BEAST/2.7/speedemon/fxtemplates/SpeedemonCollapse.xml
Cannot find merge point named sb3TreePriorTemplates from SpeedemonCollapse.xml in template. MergeWith ignored.
Investigating /Applications/BEAST 2.7.0/BEAUti.app/Contents/Resources
Investigating /Users/dawood/Library/Application Support/BEAST/2.7/starbeast3
Processing /Users/dawood/Library/Application Support/BEAST/2.7/starbeast3/fxtemplates/sb3ClockModelTemplates.xml
Cannot find merge point named sb3ClockModelTemplates from sb3ClockModelTemplates.xml in template. MergeWith ignored.
Processing /Users/dawood/Library/Application Support/BEAST/2.7/starbeast3/fxtemplates/sb3TreePriors.xml
Cannot find merge point named sb3TreePriorTemplates from sb3TreePriors.xml in template. MergeWith ignored.
Processing /Users/dawood/Library/Application Support/BEAST/2.7/starbeast3/fxtemplates/sb3SubstModels.xml
Cannot find merge point named sb3SubstModelTemplates from sb3SubstModels.xml in template. MergeWith ignored.
Processing /Users/dawood/Library/Application Support/BEAST/2.7/starbeast3/fxtemplates/StarBeast3.xml
Investigating /Users/dawood/Library/Application Support/BEAST/2.7/BICEPS
Processing /Users/dawood/Library/Application Support/BEAST/2.7/BICEPS/fxtemplates/BICEPS.xml
Processing /Users/dawood/Library/Application Support/BEAST/2.7/BICEPS/fxtemplates/YuleSkyline.xml
Investigating /Users/dawood/Library/Application Support/BEAST/2.7/BEASTLabs
Processing /Users/dawood/Library/Application Support/BEAST/2.7/BEASTLabs/fxtemplates/Weibull.xml
Processing /Users/dawood/Library/Application Support/BEAST/2.7/BEASTLabs/fxtemplates/extras.xml
Investigating /Users/dawood/Library/Application Support/BEAST/2.7/snapper
Processing /Users/dawood/Library/Application Support/BEAST/2.7/snapper/fxtemplates/snapper.xml
Investigating /Users/dawood/Library/Application Support/BEAST/2.7/ORC
Processing /Users/dawood/Library/Application Support/BEAST/2.7/ORC/fxtemplates/OptimisedRelaxedClock.xml
Investigating /Users/dawood/Library/Application Support/BEAST/2.7/BEAST.base
Investigating /Users/dawood/Library/Application Support/BEAST/2.7/BEAST.app
Processing /Users/dawood/Library/Application Support/BEAST/2.7/BEAST.app/fxtemplates/ClockModels.xml
Processing /Users/dawood/Library/Application Support/BEAST/2.7/BEAST.app/fxtemplates/ParametricDistributions.xml
Processing /Users/dawood/Library/Application Support/BEAST/2.7/BEAST.app/fxtemplates/TreePriors.xml
Processing /Users/dawood/Library/Application Support/BEAST/2.7/BEAST.app/fxtemplates/SubstModels.xml
Investigating .
connect => beastfx.app.inputeditor.BeautiConnector
subtemplate => beastfx.app.inputeditor.BeautiSubTemplate
Uniform => beast.base.inference.distribution.Uniform
Normal => beast.base.inference.distribution.Normal
OneOnX => beast.base.inference.distribution.OneOnX
LogNormal => beast.base.inference.distribution.LogNormalDistributionModel
Exponential => beast.base.inference.distribution.Exponential
Gamma => beast.base.inference.distribution.Gamma
Beta => beast.base.inference.distribution.Beta
LaplaceDistribution => beast.base.inference.distribution.LaplaceDistribution
InverseGamma => beast.base.inference.distribution.InverseGamma
prior => beast.base.inference.distribution.Prior
map
map
map
map
map
map
map
map
map
map
map
map
beauticonfig
fragment
run
Class found!
method found!
Class found!
method found!
Class found!
method found!
Class found!
method found!
Class found!
method found!
===============================================================================
Citations for this model:

Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment,
Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner,
Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut,
David Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler,
Alexei J. Drummond
  BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.
  PLoS computational biology 15, no. 4 (2019): e1006650.

===============================================================================
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?

PARTITIONS0:

[[], [], []]
Exception in Application start method
java.lang.reflect.InvocationTargetException
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at beast.pkgmgmt.launcher.BeastLauncher.run(Unknown Source)
at beast.pkgmgmt.launcher.BeautiLauncher.main(Unknown Source)
Caused by: java.lang.RuntimeException: Exception in Application start method
at javafx.graphics/com.sun.javafx.application.LauncherImpl.launchApplication1(Unknown Source)
at javafx.graphics/com.sun.javafx.application.LauncherImpl.lambda$launchApplication$2(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by: java.lang.NoClassDefFoundError: com.aquafx_project.controls.skin.AquaTabPaneSkin
at beast.pkgmgmt.MultiParentURLClassLoader.loadClass(Unknown Source)
at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Unknown Source)
at javafx.controls/javafx.scene.control.Control.loadClass(Unknown Source)
at javafx.controls/javafx.scene.control.Control.loadSkinClass(Unknown Source)
at javafx.controls/javafx.scene.control.Control$5.invalidated(Unknown Source)
at javafx.base/javafx.beans.property.StringPropertyBase.markInvalid(Unknown Source)
at javafx.base/javafx.beans.property.StringPropertyBase.set(Unknown Source)
at javafx.graphics/javafx.css.StyleableStringProperty.set(Unknown Source)
at javafx.controls/javafx.scene.control.Control$5.set(Unknown Source)
at javafx.graphics/javafx.css.StyleableStringProperty.applyStyle(Unknown Source)
at javafx.graphics/javafx.css.StyleableStringProperty.applyStyle(Unknown Source)
at javafx.graphics/javafx.scene.CssStyleHelper.transitionToState(Unknown Source)
at javafx.graphics/javafx.scene.Node.doProcessCSS(Unknown Source)
at javafx.graphics/javafx.scene.Node$1.doProcessCSS(Unknown Source)
at javafx.graphics/com.sun.javafx.scene.NodeHelper.processCSSImpl(Unknown Source)
at javafx.graphics/com.sun.javafx.scene.ParentHelper.superProcessCSSImpl(Unknown Source)
at javafx.graphics/com.sun.javafx.scene.ParentHelper.superProcessCSS(Unknown Source)
at javafx.graphics/javafx.scene.Parent.doProcessCSS(Unknown Source)
at javafx.graphics/javafx.scene.Parent$1.doProcessCSS(Unknown Source)
at javafx.graphics/com.sun.javafx.scene.ParentHelper.processCSSImpl(Unknown Source)
at javafx.controls/com.sun.javafx.scene.control.ControlHelper.superProcessCSSImpl(Unknown Source)
at javafx.controls/com.sun.javafx.scene.control.ControlHelper.superProcessCSS(Unknown Source)
at javafx.controls/javafx.scene.control.Control.doProcessCSS(Unknown Source)
at javafx.controls/javafx.scene.control.Control$1.doProcessCSS(Unknown Source)
at javafx.controls/com.sun.javafx.scene.control.ControlHelper.processCSSImpl(Unknown Source)
at javafx.graphics/com.sun.javafx.scene.NodeHelper.processCSS(Unknown Source)
at javafx.graphics/javafx.scene.Parent.doProcessCSS(Unknown Source)
at javafx.graphics/javafx.scene.Parent$1.doProcessCSS(Unknown Source)
at javafx.graphics/com.sun.javafx.scene.ParentHelper.processCSSImpl(Unknown Source)
at javafx.graphics/com.sun.javafx.scene.NodeHelper.processCSS(Unknown Source)
at javafx.graphics/javafx.scene.Node.processCSS(Unknown Source)
at javafx.graphics/javafx.scene.Scene.doCSSPass(Unknown Source)
at javafx.graphics/javafx.scene.Scene.preferredSize(Unknown Source)
at javafx.graphics/javafx.scene.Scene$2.preferredSize(Unknown Source)
at javafx.graphics/com.sun.javafx.scene.SceneHelper.preferredSize(Unknown Source)
at javafx.graphics/javafx.stage.Window$12.invalidated(Unknown Source)
at javafx.base/javafx.beans.property.BooleanPropertyBase.markInvalid(Unknown Source)
at javafx.base/javafx.beans.property.BooleanPropertyBase.set(Unknown Source)
at javafx.graphics/javafx.stage.Window.setShowing(Unknown Source)
at javafx.graphics/javafx.stage.Window.show(Unknown Source)
at javafx.graphics/javafx.stage.Stage.show(Unknown Source)
at beastfx.app.beauti.Beauti.start(Unknown Source)
at javafx.graphics/com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$9(Unknown Source)
at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runAndWait$12(Unknown Source)
at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$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)

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[higg...@gmail.com]

Thanks for the feedback: this is a bug due to the Aqua theme not being compatible with java17. The theme will be removed in v2.7.1, which is in preparation now.

If you edit the beauti.properties file in

~/Library/Application Support/BEAST/2.7/beauti.properties

and remove a line that says "thema=Aqua", then BEAUti might start again.

Hope this helps,

Remco

[Dustin Wood]

ok, that's good to know. I tried to find the file you mentioned but I don't have a BEAST directory in my Application Support directory. Could it be somewhere else?

(base) IGSWCGWBLT01026M:Application Support dawood$ ls -a

. BigFix Mozilla USGS_logo_green.png

.. CrashReporter Oracle VirtualDisplayDriver

Adobe ForeScout ProApps com.apple.TCC

App Store Gene Codes Pulse Secure iLifeMediaBrowser

Apple Google Script Editor inSync

ApplePushService JAMF SubmitDiagInfo regid.1986-12.com.adobe

BTServer Microsoft USBDisplayDriver zoom.us

To view this discussion on the web visit https://groups.google.com/d/msgid/beast-users/f81c62c3-8ef1-4500-8bbe-447b1d0ca1fen%40googlegroups.com.

[higg...@gmail.com]

This is the application support folder in your home directory (~/Library/Applications Support/) , not the root directory (/Library/Applications Support/)?

[Dustin Wood]

it works now, appreciate the help.

On Mon, Sep 26, 2022 at 7:27 PM Dustin Wood <dust...@gmail.com> wrote:

ok, got it. yeah I was looking in the root directory. Thank you!

[Dustin Wood]

ok, got it. yeah I was looking in the root directory. Thank you!