Hi Steven. I have some additional comments/suggestions regarding the GIS error you saw. First, I am curious if you are able to open the last alignment (number 7), or if you get the same error each time you try and load it.
If you can reload it, you may want to continue running the reorder from the last alignment. To do this, I'd copy the 2 fastas from alignment 7, as well as the _contigs.tab file and the _features.tab file to a clean directory, and start the reorder from these fastas just as you did originally (but to the new directory). This will create a new set of alignment directories 1-x; the last one will contain the final order. However, depending on how closely your reference and draft are related, this is likely to only move a few contigs, and might take several alignments (it relies on a history of previously seen orders that won't exist because of the restart). On the other hand, you have a lot of contigs, which might require more alignments. Also, I am not positive if it will continue producing _feature.tab files, this functionality needs to be expanded. If you can't reload it, then restarting the reorder process will likely result in the same error you saw originally. Hope that helps, and curious if reloading worked Anna Rissman ----- Original Message ----- From: "Sullivan, Steven" <steven.sulli...@nyumc.org> Date: Thursday, September 23, 2010 12:33 pm Subject: Re: [Mauve-users] java errors during Contig Mover run To: 'Aaron Darling' <aarondarl...@ucdavis.edu>, "mauve-users@lists.sourceforge.net" <mauve-users@lists.sourceforge.net> > Aaron, > > > All 7 alignment files are approximately 58 MB in size each. > > There's also plenty of disc space left (>100 GB). > > No problem displaying earlier alignments. > > > I'll send you the dataset.... > > > > --- > Steven Sullivan, Ph.D. > Bioinformatics Analyst > Dept. of Medical Parasitology > New York University Langone Medical Center > PH: (212) 263-4378 > > > -----Original Message----- > From: Aaron Darling [mailto:aarondarl...@ucdavis.edu] > Sent: Wednesday, September 22, 2010 7:39 PM > To: mauve-users@lists.sourceforge.net > Subject: Re: [Mauve-users] (no subject) > > Hi Dr. Sullivan, > > Glad to hear your contig order completed. More below... > > On Wed, 2010-09-22 at 16:40 -0400, Sullivan, Steven wrote: > > I left my first Contig Mover graphical run going overnight on a > > Windows PC, aligning ~10,000 large contigs from one new microbial > > eukaryotic genome project, to one finished reference genome from a > > closely related species, consisting of 15 chromosomes; the reference > > genome is ~25Mb . The 15 full genbank records for the chromosomes were > > in one .gbk file, the 10,000 contigs in a single multi-fasta .fna > > file. > > <snip> > > The missing whitespace warnings that were reported come from > BioJava's .gbk parser not liking some aspect of the formatting of the > genbank file. Usually the annotation will still parse and this is > not a > problem. > > > > Exception in thread “Thread-39” java.lang.Error: Inconsistency error > > at org.gel.mauve.tree.GISTree._splay(Unknown Source) > > at org.gel.mauve.tree.GISTree.splay(Unknown Source) > > <snip> > > > This may be a problem, and at the very least it will prevent you from > viewing the final alignment in the Mauve GUI. One other person has > reported the same problem to me using a different dataset but I was > unable to reproduce it and therefore unable to debug it. Possible > causes of the error include non-printing characters in the sequence or > alignment file, a corrupt alignment file (maybe the disk filled up?), > or > an as-of-yet undiscovered programming error in the alignment display > code. Can you check to ensure that the final alignment (alignment7) > is > similar in size to the previous one and confirm that it's not an issue > with disk space? Can you load earlier alignments, e.g. alignment6, > alignment5 in the display? If that doesn't lead anywhere, could you > send me the dataset (offline and in confidence of course) so I may > investigate more closely? > > Cheers, > -Aaron > > > > > > > > > ------------------------------------------------------------------------------ > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > _______________________________________________ > Mauve-users mailing list > Mauve-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mauve-users > > ------------------------------------------------------------ > This email message, including any attachments, is for the sole use of > the intended recipient(s) and may contain information that is > proprietary, confidential, and exempt from disclosure under applicable > law. 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