X11 issue on linux
Crystal
I am attempting to use Tree Annotator on a Linux machine, as I
encounter an out of memory error when using a Windows machine (1
billion generations, sampled every 1000 generations, so 1000000 trees
with 50000 trees as burnin). I keep getting an error pertaining to X11
which is not installed on my machine. Is there any way to run
TREEANNOTATOR and BEAST without X11 on Linux? Here is the error:
[lab@BTUC10 bin]$ ./treeannotator
JRI not available. Using Java bivariate attributes
Exception in thread "main" java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an
operation which requires it.
at
java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:
173)
at java.awt.Window.<init>(Window.java:437)
at java.awt.Frame.<init>(Frame.java:419)
at java.awt.Frame.<init>(Frame.java:384)
at javax.swing.JFrame.<init>(JFrame.java:174)
at jam.framework.AbstractFrame.<init>(Unknown Source)
at jam.framework.DocumentFrame.<init>(Unknown Source)
at jam.console.ConsoleFrame.<init>(Unknown Source)
at jam.console.ConsoleApplication.<init>(Unknown Source)
at jam.console.ConsoleApplication.<init>(Unknown Source)
at dr.app.tools.TreeAnnotator.main(Unknown Source)
Thank you.
-Crystal
santosh servisetti
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Andrew Rambaut
TreeAnnotator (as well as the other BEAST components) will only try to bring up a user interface if you give them no command line options.
Try typing:
./treeannotator -help
1,000,000 trees is likely to be too much for most computers and is probably more than you need. You can use logcombiner to down sample to a more manageable number (we usually suggest 10,000).
Andrew
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Andrew Rambaut
Institute of Evolutionary Biology University of Edinburgh
Ashworth Laboratories Edinburgh EH9 3JT
EMAIL - a.ra...@ed.ac.uk TEL - +44 131 6508624
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Mats Töpel
If you are running a custom installation of any GNU/Linux distribution, you will probably have some kind of X-server installed. Therefore, I think it is just the DISPLAY variable that is not set correctly.
Try setting this variable with the command:
export DISPLAY=localhost:0
... and then try starting treeannotator again.
Hope this helps
#Mats
University of Gothenburg
Department of Environmental Sciences
Phone: +46 (0) 70 406 52 92
Skype: mats.topel
Web: www.matstopel.se
Laboratory notebook: www.matstopel.se/notebook
Crystal
Thank you. I see that the memory can be increased for BEAST in Linux
via the command line, but can the same be done for TreeAnnotator?
Also, is tree annotator limited, like BEAST is, on the amount of
memory it is allowed to use? Or is the limitation the amount of memory
the computer has? Thanks again!
> ___________________________________________________________________
> Andrew Rambaut
> Institute of Evolutionary Biology University of Edinburgh
> Ashworth Laboratories Edinburgh EH9 3JT