#52 DCJ rearrangement analysis error

[seshank]

) I am trying to align two .gb files downloaded in genbank format. But it seems the Post-alignmnet analysis for SNPs doesnt work with a DCJ rearrangement analysis error
Following is the error
"Counting shared bounds between contigs/chromosomes and LCBs...done!
Counting interLCB contig/chromosome boundaries...done!
Computing signed permutations...done!
Performing DCJ rearrangement analysis...
Error

java.lang.ArrayIndexOutOfBoundsException: 0
at org.gel.mauve.assembly.AssemblyScorer.loadInfo(Unknown Source)
at org.gel.mauve.assembly.AssemblyScorer.<init>(Unknown Source)
at org.gel.mauve.assembly.ScoreAssembly$1.run(Unknown Source)
at java.lang.Thread.run(Thread.java:748)"

[Yaser Alsahafi]

I faced the same problem when aligning multiple genomes in .gb format. However, I was able to overcome it be using only on file in .gb format, which was my reference genome, and the other files in .fasta format. This was I was ablt to compute the DJC distance.

I tried to contact the email listed in the erorr, but did get any response. In interpretation,
I hope somebody could help in resolving this issue.