beauti 1.10.0 Illegal Argument Exception implement GTR model

[joan pons]

Dear users and developers,

I am using the beast version 1.10.0 and I am getting an Illegal Argument Exception "Parameter with name, gtr, is unknown" when I am trying to set a GTR model in beauti. I get this error in both manjaro 17.1 and in ubuntu 14.04 using open java. I also get the same error if I build the program from source. The error does not appear if I implement any other models of nucleotide substitution.

Any tips?

Thanks in advance,

Best

Joan

[Guy Baele]

Hi Joan,

I can't reproduce this on my Mac, not with the BEAST version I downloaded from Github and not when I build it from source.
Can you list the exact steps you take, so that I can try to obtain the same error?

Best regards,

Guy

Op maandag 9 juli 2018 12:36:54 UTC+2 schreef joan pons:

[joan pons]

Hi Guy, thanks a lot for your help.

This is the info about my system

4.14.53-1-MANJARO

JAVA VERSION
openjdk version "1.8.0_172"
OpenJDK Runtime Environment (build 1.8.0_172-b11)
OpenJDK 64-Bit Server VM (build 25.172-b11, mixed mode)


In firefox 61.0.1 (64 bits), I downloaded version from
https://github.com/beast-dev/beast-mcmc/releases/tag/v1.10.0

on terminal

tar -xvf BEAST_v1.10.0.tgz

cd BEASTv1.10.0/bin/

./beauti

import examples/Data/anolis.nex

on Sites tab Substitution Model select GTR model

select another tab and appears this pop-up window

Illegal Argument Exception
Parameter with name, gtr, is unkown

The same pop-up appears if I click Generate BEAST File

THIS IS THE MESSAGE ON TERMINAL AFTER FIRST POPUP

./beauti
java.lang.IllegalArgumentException: Parameter with name, gtr, is unknown
    at dr.app.beauti.options.PartitionOptions.getParameter(Unknown Source)
    at dr.app.beauti.options.PartitionSubstitutionModel.selectParameters(Unknown Source)
    at dr.app.beauti.options.BeautiOptions.selectParameters(Unknown Source)
    at dr.app.beauti.options.BeautiOptions.selectParameters(Unknown Source)
    at dr.app.beauti.priorspanel.PriorsPanel.setOptions(Unknown Source)
    at dr.app.beauti.BeautiFrame.setAllOptions(Unknown Source)
    at dr.app.beauti.BeautiFrame$2.stateChanged(Unknown Source)
    at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:416)
    at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270)
    at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132)
    at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67)
    at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616)
    at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591)
    at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647)
    at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279)
    at java.awt.Component.processMouseEvent(Component.java:6536)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
    at java.awt.Component.processEvent(Component.java:6304)
    at java.awt.Container.processEvent(Container.java:2239)
    at java.awt.Component.dispatchEventImpl(Component.java:4889)
    at java.awt.Container.dispatchEventImpl(Container.java:2297)
    at java.awt.Component.dispatchEvent(Component.java:4711)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4532)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
    at java.awt.Container.dispatchEventImpl(Container.java:2283)
    at java.awt.Window.dispatchEventImpl(Window.java:2746)
    at java.awt.Component.dispatchEvent(Component.java:4711)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
    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:74)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
    at java.awt.EventQueue$4.run(EventQueue.java:733)
    at java.awt.EventQueue$4.run(EventQueue.java:731)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
    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)

[Guy Baele]

Hi Joan,

I think the versions for Mac must have been updated already since the release, but this may not have been the case for the other downloads.

As a workaround for this problem, after you have selected the GTR model, go to the Priors panel and make sure the option 'Use classic priors/operators' is selected.
Then it should work fine.

Best regards,
Guy

Op woensdag 11 juli 2018 14:40:14 UTC+2 schreef joan pons:

[joan pons]

Thanks Guy,

the tip solved the problems

[joan pons]

Hi Guy,

It sounds very rare but again I get an gtr argument exception even if a select 'Use classic priors/operators'.

Best,

Joan

[lau...@cobcan.es]

Dear Guy,

I am using beast in ubuntu and I had the same problem that Joan (Illegal Argument Exception "Parameter with name, gtr, is unknown")., When I go to Priors panel and I select "Use classic priors/operators" I get an gtr argument exception but appears this pop-up window

Illegal Argument Exception
Operator with name, uniformPlnv, is unknown

The error does not appear if I dont select "Use classic priors/operatos"

Any idea about a possible solution?

Thanks in advance,

Best

Laura 

[Guy Baele]

We are working on releasing BEAST v1.10.1, which should take care of this issue.
I can't reproduce it myself on Linux using the latest version.

Best regards,
Guy

Op donderdag 19 juli 2018 21:09:35 UTC+2 schreef lau...@cobcan.es: