#54 Mauve Contig Mover: getting error while reordering genbank output

[Kazi Ahsan]

Hi,

I am trying to reorder a draft assembly based on a reference genome using the Mauve Contig Mover. I have used genbank output from prokka annotation for the draft and the referene is downloaded from NCBI. I am receiving this error:

Any suggesstions will be apprecieted.

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$2.nextSequence(Unknown Source)
at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source)
at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source)
at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source)
at org.gel.mauve.XmfaViewerModel.init(Unknown Source)
at org.gel.mauve.XmfaViewerModel.<init>(Unknown Source)
at org.gel.mauve.ModelBuilder.buildModel(Unknown Source)
at org.gel.mauve.gui.FrameLoader.loadFile(Unknown Source)
at org.gel.mauve.gui.FrameLoader.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: 12
at java.lang.String.substring(Unknown Source)
at org.biojava.bio.seq.io.GenbankContext.processHeaderLine(GenbankContext.java:310)
at org.biojava.bio.seq.io.GenbankContext.processLine(GenbankContext.java:129)
at org.biojava.bio.seq.io.GenbankFormat.readSequence(GenbankFormat.java:146)
at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:105)
... 10 more
initing data
printing
printing
done: C:\Users\ahsan\Mauve_output\ref_vs_NZ1_GBK\alignment1\NZ_Bl_01_BLSV_a1.gbk_contigs.tab
Exception in thread "Thread-8" java.lang.NullPointerException
at org.gel.mauve.MauveHelperFunctions.getFeatures(Unknown Source)
at org.gel.mauve.contigs.ContigReorderer.output(Unknown Source)
at org.gel.mauve.contigs.ContigReorderer.initMauveData(Unknown Source)
at org.gel.mauve.contigs.ContigReorderer.initModelData(Unknown Source)
at org.gel.mauve.contigs.ContigReorderer$ReordererMauveFrame$1.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)