[Mauve-users] Annotations not loading

[Eun J. Na <en...@co...>]

Dear All,

Any suggestion to successfully load the annotations from the .gbk file?
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For more background, I am aligning eleven bacterial genomes using
progressiveMauve, and much to my delight, succeeded in doing so!

Except that the annotations from the .gbk file won't load. I read through
the email archive and accordingly have tried clearing alignment cache, but
that doesn't seem to help.

The error message I received is as follows:

1월 25, 2017 9:55:25 오후 java.util.prefs.WindowsPreferences <init>
WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at
root 0x80000002. Windows RegCreateKeyEx(...) returned error code 5.
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)
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:310)
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 feedback would be much appreciated, as being able to see the annotation
results directly in Mauve would make things much easier for me. Thank you!

Best,
Eun Jung