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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Any advice would be appreciated
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