Hi.

I'm using mauve to align an organism's assembly I made against the organism's NCBI assembly. When I first did it the output graph included annotations from the NCBI assembly, but since then I was not able to get the annotations to appear on the graph. For example, I got the following :

mauve output

I looked at mauve's console and it showed the following error message:

java.io.IOException: Empty alignment file.  If the alignment file was generated by Mauve then the genomes may be unrelated.
        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(Thread.java:745)

I don't understand this message since the graph shows an alignment. I'd love to your thoughts about this issue.

Thanks.