Hello, I'm using Mauve on a windows 7 64 (Java 64) machine. After using the "Oh skeethocky mushrooms" fix of using the latest development snapshot (20120303), and fixing the side-by-side error present in the Windows build (by changing the version in the manifest file to match: 8.0.50727.6195 (the .6195 was listed as something else originally).), I got MCM to move forward on aligning my draft genome to a reference genome with default settings (both genomes approx 1 G).
After ~12 hours, it seems to have completed alignment 1 but then runs out of memory: ... ..... Organisms have 41.2% GC Completed without error Alignment complete! file:/C:/Program%20Files%20(x86)/Mauve%2020120303/Mauve.jar!/images/Dcj16.gif made reorder frame shown Exception in thread "Thread-7" 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) etc. So. I have files in an alignment1 folder. These include the original draft and reference fasta files, a .sslist file for each, alignment1 (no file type given for this 4G file. I'm not sure what is contained in this file, or how to open it to see), alignment1.backbone, alignment1.bbcols, alignment1.guide_tree. That's it. It didn't seem to make any of the other files that the I was supposed to get as an output. Any idea what's going on or what I can do about it? I have 16 GB Ram, 4 processor cores. In the end, I hoped to have a fasta file containing a my draft genome in simple chromosomes (from its alignment to the reference chromosome genome). Is that an output that I should expect? Thanks so much! -Lucinda ------------------------------------------------------------------------------ Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery and much more. Keep your Java skills current with LearnJavaNow - 200+ hours of step-by-step video tutorials by Java experts. SALE $49.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122612 _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
