Hi Gerald, This definitely sounds like an issue with your GenBank file -- I've found that Mauve's GenBank parser is peculiarly picky about the format of the file's header. By comparing a problem file with one that works, you can often figure out what the issue is. If you are stumped, and are willing to send me a copy of the file in question, I can take a look at it off-list ...
Cheers, Guy Dr. Guy Plunkett III Senior Scientist, Genome Center of Wisconsin Senior Scientist, DNASTAR http://www.genome.wisc.edu/information/gplunkett.html On 5/7/14, Lackner Gerald wrote: >Hi Aron, > >thank you very much for your reply. I have finally figured out that Mauve >works fine when I use other input files, e.g. multi fasta files of my genomes. >Genbank files from other test genomes work as well. Maybe something is >illegal in the Genbank files of my genomes. Indeed, I received the following >error message using a (reformatted) genbank file. > >Error reading file. >org.biojava.bio.BioException: Could not read sequence > at > org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:108) > at org.gel.mauve.format.BaseFormat$2.nextSequence(Unknown Source) > at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source) > at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source) > at org.gel.mauve.GenomeBuilder.buildGenome(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) > >I do you have any suggestions, how I could preserve me annotations? > >Best, > >Gerald ------------------------------------------------------------------------------ Is your legacy SCM system holding you back? Join Perforce May 7 to find out: • 3 signs your SCM is hindering your productivity • Requirements for releasing software faster • Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
