Ray,
I am using the Linux version. I've already adjusted that parameter to
account for the RAM capacity of the workstation. I'm wondering if there is
a similar parameter for max similarity index that can be adjusted. If so
adjusted to what?
-Amarin
On Thu, Oct 9, 2014 at 12:45 AM, Raymond Wan <r...@cuhk.edu.hk> wrote:
>
> Hi Amarin,
>
> I'm not sure if this will solve your problem, but are you running the Linux
> version? If you are and running the script called "Mauve", it is actually
> a
> bash script that in turn calls Java. You can view it and adjust the memory
> requirements.
>
> For example, in the script, I see:
>
> JAVA_ARGS="-Xms200M -Xmx500M"
>
> which sets the minimum and maximum amount of memory used. I'm not sure if
> Windows is the same.
>
> Ray
>
>
> Quoting Amarin Cogburn <amarin.cogb...@gmail.com>:
>
> > Is there value I can adjust to allow more memory for this function? I
> > aligned 3 1.2GB genomes but am unable to open the alignment file in the
> > mauve GUI. If this is not possible could anyone recommend a different
> > application to use for visualization? Thanks.
> >
> > Exception in thread "Thread-1" java.lang.RuntimeException: Similarity
> index
> > is too large.
> > at org.gel.mauve.SimilarityIndex.allocateIndex(Unknown Source)
> > at org.gel.mauve.SimilarityIndex.<init>(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:745)
> >
>
>
>
>
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>
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