Sorry for sending another message since this has been so active 
recently, but I have a genome genbank file that I downloaded from JGI 
that does not display the annotation in the alignment view.  The file is 
readable by artemis and shows all of the annotation, so I assume that it 
is in the correct format.  I have been able to view the annotations from 
other genomes that I downloaded from JGI, so I am not sure what the 
problem is.  Below is the error message that I get.  Any suggestions on 
what is wrong would be appreciated.

Sincerely,

Jason Flowers



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(BaseFormat.java:113)

    at org.gel.mauve.GenomeBuilder.buildGenome(GenomeBuilder.java:175)

    at org.gel.mauve.GenomeBuilder.buildGenome(GenomeBuilder.java:105)

    at org.gel.mauve.GenomeBuilder.buildGenome(GenomeBuilder.java:59)

    at org.gel.mauve.XmfaViewerModel.init(XmfaViewerModel.java:151)

    at org.gel.mauve.XmfaViewerModel.<init>(XmfaViewerModel.java:43)

    at org.gel.mauve.ModelBuilder.buildModel(ModelBuilder.java:284)

    at org.gel.mauve.gui.FrameLoader.loadFile(FrameLoader.java:87)

    at org.gel.mauve.gui.FrameLoader.run(FrameLoader.java:57)

    at java.lang.Thread.run(Unknown Source)

Caused by: java.lang.StringIndexOutOfBoundsException: String index out 
of range: 12

    at java.lang.String.substring(Unknown Source)

    at 
org.biojava.bio.seq.io.GenbankContext.processHeaderLine(GenbankContext.java:308)

    at 
org.biojava.bio.seq.io.GenbankContext.processLine(GenbankContext.java:129)

    at 
org.biojava.bio.seq.io.GenbankFormat.readSequence(GenbankFormat.java:146)

    at 
org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:105)

    ... 10 more

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 From must be less than To:                 /function="


Any advice would be appreciated

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