Tracer SkyGrid Analysis Java Error

[Matt Wersebe]

Hello, 

I working on estimating the the EPS history for a viral gene sequence using SkyGrid. I ran my BEAST (v1.10.4) chain for 100Million logging states every 10K iterations. Looking at the trace, everything that seems to have converged well with high ESS (>200) across all the parameters. 

When I run the SkyGrid analysis in tracer using the options noted below in the screen shot, I get a cryptic java error which I cannot resolve. I have pasted the java error below which is output only when I launch tracer from the command line using java -jar tracer.jar. 

Any insights would be greatly appreciated!

Thanks!

java -jar .\tracer.jar
Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: -1
        at java.util.ArrayList.elementData(Unknown Source)
        at java.util.ArrayList.get(Unknown Source)
        at dr.inference.trace.LogFileTraces.getTrace(Unknown Source)
        at tracer.analysis.SkyGridDialog.addToTemporalAnalysis(Unknown Source)
        at tracer.analysis.SkyGridDialog.createSkyGridFrame(Unknown Source)
        at tracer.application.TracerFrame.doSkyGrid(Unknown Source)
        at tracer.application.TracerFrame$19.actionPerformed(Unknown Source)
        at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
        at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
        at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
        at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
        at javax.swing.AbstractButton.doClick(Unknown Source)
        at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
        at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
        at java.awt.Component.processMouseEvent(Unknown Source)
        at javax.swing.JComponent.processMouseEvent(Unknown Source)
        at java.awt.Component.processEvent(Unknown Source)
        at java.awt.Container.processEvent(Unknown Source)
        at java.awt.Component.dispatchEventImpl(Unknown Source)
        at java.awt.Container.dispatchEventImpl(Unknown Source)
        at java.awt.Component.dispatchEvent(Unknown Source)
        at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
        at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
        at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
        at java.awt.Container.dispatchEventImpl(Unknown Source)
        at java.awt.Window.dispatchEventImpl(Unknown Source)
        at java.awt.Component.dispatchEvent(Unknown Source)
        at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
        at java.awt.EventQueue.access$500(Unknown Source)
        at java.awt.EventQueue$3.run(Unknown Source)
        at java.awt.EventQueue$3.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
        at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
        at java.awt.EventQueue$4.run(Unknown Source)
        at java.awt.EventQueue$4.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
        at java.awt.EventQueue.dispatchEvent(Unknown Source)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.run(Unknown Source)