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
