Hello, I have created a MSA using clustal omega and use iqtree to calculate the phylogenetic tree. However, I am having a hard time to load the associated tree file. Whenever I tried to load the tree file, a pop-up window came up and showed the message problem loading tree file and null in the context. I have made sure that the tree file is in newick tree format. There are about 500 sequences in the files. Would appreciate any help on trying to link the two files.
Hi cccjon,
Are you first opening the MSA into Jalview, and using the
File → Load Associated Tree…
menu option on the MSA window open to open the tree file, and are you selecting the FILENAME.treefile file that iqtree outputs?
If you’re already doing that, could you try it again, but before opening the tree file, open the Java Console window by going to Tools → Show Java Console, then in the “Jalview Java Console” window that appears click on the “Clear” button, and select Log level “DEBUG”. Then open the tree file as above.
If there’s some output in the Java Console, could you copy it and paste it into a comment here?
Thanks, Ben
Hello Ben,
Thanks for helping! I tried it one more time and it still does not work. The following is what comes up in the console. I do use the .treefile as the tree file. I did not edit the file after downloading it from iqtree. The only thing I have done on the .treefile is opening it with FigTree.
Jalview Version: 2.11.2.6
Jalview Installation: Source git-commit:d5bd34eb49 [releases/Release_2_11_2_Branch]
Build Date: 21:12:02 23 January 2023
Java version: 1.8.0_202
x86_64 Mac OS X 10.16
Install4j version: null
Install4j template version: null
Launcher version: 1.8.3-1.2.9_JVL
LookAndFeel: FlatLaf Light (com.formdev.flatlaf.FlatLightLaf)
java.io.IOException: NewickFile: Can’t parse bootstrap value at position 65 ( ((((2730 )
at jalview.io.NewickFile.parse(NewickFile.java:607)
at jalview.gui.AlignFrame.showNewickTree(AlignFrame.java:4151)
at jalview.gui.AlignFrame.showNewickTree(AlignFrame.java:4121)
at jalview.gui.AlignFrame.showNewickTree(AlignFrame.java:4115)
at jalview.gui.AlignFrame$19.run(AlignFrame.java:4091)
at jalview.io.JalviewFileChooser.handleResponse(JalviewFileChooser.java:619)
at jalview.io.JalviewFileChooser.showOpenDialog(JalviewFileChooser.java:234)
at jalview.gui.AlignFrame.loadTreeMenuItem_actionPerformed(AlignFrame.java:4110)
at jalview.jbgui.GAlignFrame$66.actionPerformed(GAlignFrame.java:1136)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$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 javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:842)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:886)
at java.awt.Component.processMouseEvent(Component.java:6539)
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:4535)
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)
java.lang.NullPointerException
at jalview.gui.AlignFrame$19.run(AlignFrame.java:4091)
at jalview.io.JalviewFileChooser.handleResponse(JalviewFileChooser.java:619)
at jalview.io.JalviewFileChooser.showOpenDialog(JalviewFileChooser.java:234)
at jalview.gui.AlignFrame.loadTreeMenuItem_actionPerformed(AlignFrame.java:4110)
at jalview.jbgui.GAlignFrame$66.actionPerformed(GAlignFrame.java:1136)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$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 javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:842)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:886)
at java.awt.Component.processMouseEvent(Component.java:6539)
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:4535)
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)
Hi cccjon,
Thanks for the diagnostic info. I’ve had a go with an example MSA with iqtree both online and cmdline (and also exported as Newick through figtree), and the Newick files generated all seem okay. Yours appears to be failing to parse properly so there must be something specific in the syntax. Would you be willing to share the .treefile either in this thread or you could message me directly and attach the file? We can then have a look and see if our Newick parser needs to be updated, or if there’s some other problem at play!
Thanks, Ben
Hello Ben,
I don’t seem to be able to upload my tree file. Below is the thing in the file.
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Hi cccjon,
Thanks for pasting that. I think maybe our discussion forum is reluctant to upload files with an unknown (to it) file extension, but your pasted copy is fine.
You’ll be pleased to hear I’m getting the same Exception, which should be enough to go on trying to fix it. I can’t see a quick workaround straight away so we’ll see if we can get a patch out for it soon, apologies to not have an immediate fix for you.
Ben
Hi !
Whilst @ben_soares looks at exactly what’s up with Jalview’s newick parser, I’d recommend loading your tree into figtree, exporting as a simple newick, then try to load that into Jalview. It looks to me as if bootstraps might need to be formatted before jalview can read them.
We also have an experimental version of jalview linked to archeopteryx that should be able to handle the file.
Jim.
This bug is being tracked on issue JAL-4132