#55 Score an assembly Error

[Pat]

Dear all,

I am trying to get the scores for an aligment with progressiveMAUVE, but I get an error message, please see below. Could you please help me with the error? Totally stuck at this stage. I tried to run the same sequences in Linux and in Wondows, both returned similar error messages. The alignment works fine, the software gets stuck during the scoring.

Many thanks in advance for your input.

Pat

LINUX ERROR MESSAGE:
mauve_snapshot_2015-02-13

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)</init>

WINDOWS ERROR MESSAGE:
mauve_snapshot_2015-02-26

Sep 04, 2018 1:14:16 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.
Counting shared bounds between contigs/chromosomes and LCBs...done!
Counting interLCB contig/chromosome boundaries...done!
Computing signed permutations...
Error</init>

java.lang.ArrayIndexOutOfBoundsException: 1
at org.gel.mauve.analysis.PermutationExporter.computeSignedPermutation(Unknown Source)
at org.gel.mauve.analysis.PermutationExporter.getPermStrings(Unknown Source)
at org.gel.mauve.analysis.PermutationExporter.getPermStrings(Unknown Source)
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(Unknown Source)</init>