Hi again Brianna, The alignment is complete, and the error you observed occurs because the alignment viewer is not really engineered to display alignments of such large sequences. It is certainly possible to allocate more memory to java to get past the error you encountered by changing the -Xmx argument in the script that launches Mauve, but I wouldn't be surprised if you encounter other issues. Even if you can't browse the alignment in the Mauve viewer, the alignment can be used for any other purposes you have in mind.
Best, -Aaron On Tue, 2013-09-17 at 09:59 +1000, Brianna Flynn wrote: > Hello, > I had just written previously about the speed and progression of my > alignment. It seems, however, that since that point the alignment may > have finished, but I am not sure what to do about the error message > that is coming up now: > ...done. > root alignment has 85351 superintervals > root alignment length: 3971048854 > Organisms have 39.1% GC > Completed without error. > Sep 16, 2013 6:55:52 PM java.util.prefs.FileSystemPreferences$2 run > INFO: Created user preferences directory. > Exception in thread "Thread-8" java.lang.OutOfMemoryError: Java heap > space > at org.gel.mauve.tree.TreeStore.resizeArrays(Unknown Source) > at org.gel.mauve.tree.TreeStore.createGistNode(Unknown Source) > at org.gel.mauve.tree.GISTree.insert(Unknown Source) > at org.gel.mauve.XMFAAlignment.<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(Unknown Source) > > > There was another thread previously > here https://sourceforge.net/mailarchive/message.php?msg_id=30360833 that > addressed the same question, but no resolution seems to have been obtained > unless I just cannot see the response for some reason. In any case, my issue > is similar in that I have files in my alignment folder that include the > original draft genome, the mm10 mouse fasta, a .sslist file for each of the > genomes just mentioned, the original file that I indicated for output but > which does not have a file extension, also a .backbone file, a .bbcols file, > and the .guide_tree file. The file without the extension appears to be the > XMFA file but I am not sure. If I'm going by the output files listed on the > source page, I seem to be missing a few. The program is not indicated as > running anymore on the computer's processes, but I am not sure how to remedy > this error, what it exactly means, or it my alignment is complete. My main > concern is whether or not the alignment is complete and if I have the correct > files. > > > Any elucidation on this error would be greatly appreciated. > > > Thank you, > Brianna Flynn > > > -- 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. ------------------------------------------------------------------------------ LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
