TreeAnnatotor in terminal

[Michael Harvey]

Hi,

I've been trying to run TreeAnnotator from the command line but I'm receiving the following error:

Command:

java -Xmx1024m -Xms1024m -cp ./lib/beast.jar dr.app.tools.TreeAnnotator

Stdout:

Exception in thread "main" java.lang.NoClassDefFoundError: dr/app/tools/TreeAnnotator

Caused by: java.lang.ClassNotFoundException: dr.app.tools.TreeAnnotator

at java.net.URLClassLoader$1.run(URLClassLoader.java:202)

at java.security.AccessController.doPrivileged(Native Method)

at java.net.URLClassLoader.findClass(URLClassLoader.java:190)

at java.lang.ClassLoader.loadClass(ClassLoader.java:307)

at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)

at java.lang.ClassLoader.loadClass(ClassLoader.java:248)

I see others have had similar issues (mostly in Linux), but I haven't been able to find a solution for my machine (mac os 10.6).

Thanks for any assistance,

Mike Harvey

mha...@lsu.edu

[Andrew Rambaut]

Hi Mike,

What this means is that Java isn't finding the beast.jar file where you said it was ('./lib/beast.jar'). The

simplest way is to specify the full path to where ever you have installed beast. Something like:

java -Xmx1024m -Xms1024m -cp /usr/local/BEAST/lib/beast.jar dr.app.tools.TreeAnnotator

Change the '/usr/local/BEAST/' to the directory where beast is residing.

Best,

Andrew

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[Michael Harvey]

Andrew,

Thanks for the quick response. I worked around the issue by using an older version of BEAST (1.6 instead of 2), which works without error. Unfortunately, the path doesn't seem to be the issue with BEAST 2, as specifying the complete path (java -Xmx1024m -Xms1024m -cp /Applications/BEAST 2.0.2pre/lib/beast.jar dr.app.tools.TreeAnnotator) gives the same error, and I am able to run BEAST without error in the command line using that path.

Thanks,

Mike

[Andrew Rambaut]

Mike,

The path below has a space in it. You will need to use '\ ' to say this is is part of the path rather than two different arguments on the command line.

Andrew

[Remco Bouckaert]

The class name dr.app.tools.TreeAnnotator is for version 1 and it looks like you are using the jar file for version 2.
For version 2, the class name changed to beast.app.treeannotator.TreeAnnotator, so that explains the ClassNotFoundException.

Also, the class is currently part of the beastii addon, so you have to add BEASTii.addon.jar in your class path as well. What should work is

java -Xmx1024m -Xms1024m -cp ./lib/beast.jar:$(path to BEASTii)/lib/BEASTii.addon.jar beast.app.treeannotator.TreeAnnotator

where you replace $(path to BEASTii) with the actual path to where the BEASTii add-on is installed -- which is probably /Users/$(your user name)/Library/Application Support/BEAST/BEASTii on a Mac.

Remco