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?
Cheers,
Guy
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