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
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