Hello Franz, thanks for reporting this. You are not the only person experiencing this issue with Mauve 2.4.0. It looks like a bug! I am planning to take a close look and work on a fix just as soon as Australian grant-writing deadlines pass in a couple weeks.
Best, -Aaron On Tue, 2015-02-10 at 16:22 +0100, Franz Baumdicker wrote: > Hi, > > I am trying to align the core genes (~1000 genes) of 41 small bacterial > genomes. However, depending on the input order I am getting a lot of > scoring error messages or no errors. > Unfortunately I didn't find an input order for all 41 genomes which > produces no errors. > In addition I found two sequence files where even > progressiveMauve --output=outfile seq1.faa seq2.faa > produces scoring errors while > progressiveMauve --output=outfile seq2.faa seq1.faa > does not. > > I am using version 2.4.0 on Linux. In version 2.3.1 no scoring errors > show up, but progressiveMauve gets caught in an endless loop for the > same input orders. > > What does scoring error mean? > Is there any way to predict which order of sequences will produce > scoring errors and which doesn't? > Or even better is there a way to modify the input data to prevent the > scoring error at all? > > Greetings, > > Franz Baumdicker > > ------- > Dr. Franz Baumdicker > Math. Institut > Eckerstr 1 > 79106 Freiburg > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming. The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. http://goparallel.sourceforge.net/ > _______________________________________________ > Mauve-users mailing list > Mauve-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mauve-users -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. ------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
