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. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= ------------------------------------------------------------------------------ Nokia and AT&T present the 2010 Calling All Innovators-North America contest Create new apps & games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
