beauti from version v.2.7.x won't save xml file about beast2 HOT 3 OPEN

Thanks for the bug report Julia.

It is a bit of a mystery what is happening here, since I have not been able to reproduce the problem with Windows 10 and v2.7.3: importing any alignment, then File/Save and type x produces the file x.xml. Perhaps it is something specific to the packages you have installed?

When you go to the Help/Messages menu, do you see any report of error messages there when saving (especially at the end of the list of messages)? Perhaps there is a clue there to what might be going wrong.

Remco

from beast2.

Hi Remco,

thank you for your reply. It's a java error actually

"Probing: starbeast3.addon.jar Exception in thread "JavaFX Application Thread" java.lang.OutOfMemoryError: Java heap space"

I've tried to follow what you suggested in a previous post by can't seem to get this to work:

java -Xmx8g -cp C:\ProgramFiles\BEAST.v2.7.3\lib\launcher.jar beast.pkgmgmt.launcher.BeautiLauncher

it returns a "java.lang.ClassNotFoundException: beastfx.app.beauti.Beauti" error

Any tips are much appreciated!
Thanks!

Julia

from beast2.

Hi Julia,

Probably the easiest way to increase memory (which is indeed what the error message indicates is necessary) is to edit the batch file in \path\to\BEAST\bat\BEAUti.bat, (where \path\to\BEAST is the path to where you have BEAST installed).

Line 7 says

    "%~dp0\..\jre\bin\java" -Dfile.encoding=UTF-8 -cp "%~dp0\..\lib\launcher.jar" beast.pkgmgmt.launcher.BeautiLauncher %*

and if you add -Xmx16g as argument to java, like so

    "%~dp0\..\jre\bin\java" -Xmx16g -Dfile.encoding=UTF-8 -cp "%~dp0\..\lib\launcher.jar" beast.pkgmgmt.launcher.BeautiLauncher %*

it should reserve 16GB of memory. To start BEAUti, run path\to\BEAST\bat\BEAUti.bat from the command prompt.

By default, 8GB is reserved for BEAUti when launched via the icon, so changing it to 16GB makes more sense than keeping it 8GB.

Hope this helps,

Remco

from beast2.