Thanks, Aaron. Worked like a charm. - Guy On 10/5/10, Aaron Darling wrote: >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
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