search

bioDS / beast-phylonco

A BEAST2 package for single-cell cancer evolution
GNU Lesser General Public License v2.1
6 stars 2 forks source link

Methylation Beauti template not working #8

Closed kche309 closed 2 years ago

kche309 commented 2 years ago

The template MethylationHKY.xml generates a beast.util.XMLParserException when loading a nexus file beast2/examples/nexus/64.nex into Beauti using BEAST v2.6.6, Phylonco v0.0.5.

Current workaround: Delete the template MethylationHKY.xml from the package installation templates folder.

For Windows in Users\<username>\BEAST\2.x\Phylonco\templates
For Mac in /Users/<username>/Library/Application Support/BEAST/2.x/Phylonco/templates
For Linux in /home/<username>/.beast/2.x/Phylonco/templates

See full error message below:

beast.util.XMLParserException: 
Error 1017 parsing the xml input file

Class could not be found. Did you mean beast.app.beauti.BeautiConfig?
Perhaps a package required for this class is not installed?

Error detected about here:
  <beast>
      <plugin id='MethylationHKY.s:64' spec='MethylationHKY'>

    at beast.util.XMLParser.createObject(XMLParser.java:911)
    at beast.util.XMLParser.parseTemplate(XMLParser.java:501)
    at beast.app.beauti.BeautiSubTemplate.createSubNet(BeautiSubTemplate.java:372)
    at beast.app.beauti.BeautiSubTemplate.createSubNet(BeautiSubTemplate.java:307)
    at beast.app.beauti.BeautiDoc.createInput(BeautiDoc.java:1726)
    at beast.util.XMLParser.createBeastObject(XMLParser.java:1015)
    at beast.util.XMLParser.createObject(XMLParser.java:930)
    at beast.util.XMLParser.parseTemplate(XMLParser.java:501)
    at beast.app.beauti.BeautiSubTemplate.createSubNet(BeautiSubTemplate.java:372)
    at beast.app.beauti.BeautiSubTemplate.createSubNet(BeautiSubTemplate.java:338)
    at beast.app.beauti.BeautiDoc.addAlignmentWithSubnet(BeautiDoc.java:1502)
    at beast.app.beauti.BeautiAlignmentProvider.addAlignments(BeautiAlignmentProvider.java:218)
    at beast.app.beauti.BeautiAlignmentProvider.getAlignments(BeautiAlignmentProvider.java:174)
    at beast.app.beauti.BeautiAlignmentProvider.getAlignments(BeautiAlignmentProvider.java:111)
    at beast.app.beauti.Beauti$1.actionPerformed(Beauti.java:876)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
    at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
    at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
    at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
    at com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:125)
    at java.awt.MenuItem.processActionEvent(MenuItem.java:669)
    at java.awt.MenuItem.processEvent(MenuItem.java:628)
    at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:357)
    at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:345)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:763)
    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)
Validation error when initializing object beast.evolution.sitemodel.SiteModel (id SiteModel.s:64):
java.lang.IllegalArgumentException: Input 'substModel' must be specified.
    at beast.core.Input.validate(Input.java:757)
    at beast.core.BEASTInterface.validateInputs(BEASTInterface.java:478)
    at beast.util.XMLParser.createObject(XMLParser.java:936)
    at beast.util.XMLParser.parseTemplate(XMLParser.java:501)
    at beast.app.beauti.BeautiSubTemplate.createSubNet(BeautiSubTemplate.java:372)
    at beast.app.beauti.BeautiSubTemplate.createSubNet(BeautiSubTemplate.java:338)
    at beast.app.beauti.BeautiDoc.addAlignmentWithSubnet(BeautiDoc.java:1502)