Mauve export ortholog difficulties

Question

[mgazdik33]

Hello

After using Illumina and de novo assembly on 23 bacterial genomes, I have used Mauve to reorder my assembled contigs and generated an alignment of 23 genomes plus on reference genome. I would like to have Mauve export the orthologs of the alignment so that I can examine phylogeny of these isolates however when I go to tools --> export orthologs I get the following error message:

Jan 16, 2015 2:23:46 PM 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 checking for updates.
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries
Warning: whitespace found between sequence entries

It generates two files however both are empty.

Any direction would be appreciated. Thanks