Hi Amarin, Ray, In addition to changing the the -Xmx parameter for the java heap size, in this case you'll also need to change a parameter in the class org.gel.mauve.SimilarityIndex (2.3.1 release) or the class org.gel.mauve.histogram.ZoomHistogram (current svn trunk). The specific variable is max_index_mb in that class. In the current svn trunk it's set to 300, and could be set much higher if you have adjusted the -Xmx accordingly. Of course, this means you'll need to check out the source code and build it. Mauve uses and ant build file. A replacement Mauve.jar can be built simply by running `ant jar` in the source code directory (assuming you have ant and its dependencies installed).
Best, -Aaron On Fri, 2014-10-10 at 00:02 +1100, Amarin Cogburn wrote: > 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) > > > > > > > > ------------------------------------------------- > This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk > > > -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. ------------------------------------------------------------------------------ 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
