TreeAnnotator v1.5.3 (java heap space error)

[Fuat Ozyoruk]

Dear All,

I have large data set and and a file created by Beast (3.5GB). After a while TreeAnnotator v1.5.3 started, I am getting an error message "java.lang.outofmemory error: Java Heap space" which you can find attached in more detail. I have already identifed that this error is not due to computer capability.

Any help will be greatly appreciated

Fuat 

 

[Baarlen, Peter van]

Dear Fuat et al.,

 

I had the same error message months ago; your Beast output file is too large for the available amount of (RAM) memory to be handled by Java/TreeAnnotator. I could not increase memory anymore (not physically, nor by making more RAM available to Java to use) on my windows system. However, I found that an earlier version of TreeAnnotator (in my case, the one that came with Beast 1.5.1) could properly process the Beast output file and generate a treefile. You could ask your system manager if it is possible to increase RAM on your system or try earlier TreeAnnotator versions.

 

best wishes,

 

Peter.

 

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From: beast...@googlegroups.com [mailto:beast...@googlegroups.com] On Behalf Of Fuat Ozyoruk
Sent: maandag 1 maart 2010 16:22
To: beast-users
Subject: TreeAnnotator v1.5.3 (java heap space error)

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[Simon Greenhill]

Hi Fuat,

By default Java is only allocated a certain amount of memory by the
operating system. You can easily increase the amount of RAM available
to the BEAST applications by following the instructions here:
http://beast.bio.ed.ac.uk/Increasing_Memory_Usage

However, rather than doing this for BEAST, you'll need to do the same
for TreeAnnotator. Unfortunately TA is prepackaged, and - as far as I
can tell - you'll probably need to install the source code and compile
it manually to do this (not hard on Linux or OSX).

Another alternative is to use the LogCombiner application to resample
the trees at a lower frequency.

--Simon

[Andrew Rambaut]

Dear Fuat (thanks for responding Simon),

The instructions on the page indicated should also apply for TreeAnnotator and is relatively easy for Mac and Linux/UNIX. Unfortunately, I don't think it is possible to alter the Windows exectutable in this way. However, you can still run TreeAnnotator from the command line. You need to use the following:

java -Xmx1024M -cp lib/beast.jar dr.app.tools.TreeAnnotator

(the 1024M specifies a GB of memory but use more if needed).

The final point is that I notice you are trying to analyse 124601 trees. This is probably a lot more than you need as they will be correlated (depending on the actual data, it may require more memory than you have available). Using LogCombiner to 'thin' these out to about 10000 trees will help.

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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[Chanelle]

Dear Andrew

Is the command, as you specified it to Fuat, a command line switch?
Can you please give my the full command as I need to type it to make it run on my computer.
I'm using Windows.

It will be much appreciated

Chaelle