Hi Guy, On Mon, 2010-10-04 at 11:57 -0500, Guy Plunkett III wrote: > I am trying to view an existing Mauve alignmnet of 41 E. coli genomes, and > repeatedly get an OutOfMemoryError after 37 of the 41 sequences have been > read. The console message, after the obligatory lines of "Warning: whitespace > found between sequence entries" reads: > > Exception in thread "Thread-3" java.lang.OutOfMemoryError: Java heap space > at org.gel.mauve.format.DelegatingSequence.init(Unknown Source) > at org.gel.mauve.format.DelegatingSequence.<init>(Unknown Source) > at org.gel.mauve.format.BaseFormat.makeDelegate(Unknown Source) > at org.gel.mauve.format.BaseFormat$2.nextSequence(Unknown Source) > at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source) > at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source) > at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source) > at org.gel.mauve.XmfaViewerModel.init(Unknown Source) > at org.gel.mauve.XmfaViewerModel.<init>(Unknown Source) > at org.gel.mauve.ModelBuilder.buildModel(Unknown Source) > at org.gel.mauve.gui.FrameLoader.loadFile(Unknown Source) > at org.gel.mauve.gui.FrameLoader.run(Unknown Source) > at java.lang.Thread.run(Thread.java:637) > > Mauve 2.3.1 build 18 (64 bit), Mac OS X 10.6.4, 4 GB RAM > > Is there any way to alot more memory to the alignment viewer? >
The max amount of Java memory used by Mauve on Mac OS X is specified in a file called Info.plist inside the Mauve.app/Contents folder. This file can be edited from the command-line, simply by switching into the above-listed directory and opening the file in your favorite text editor. Once the file is opened, look for some lines like: <key>VMOptions</key> <string>-Xmx500m</string> And change 500m to something big, like 2000m or bigger if you machine has the memory for it and you're using 64-bit Java. Save the file, re-launch Mauve, and hopefully it will now load the big alignment. -Aaron ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
