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) > ------------------------------------------------- This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk ------------------------------------------------------------------------------ Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
