Hello,
I was trying to score my assembly with Mauve assembly metrics, but the run was
not completed. It seems to have started out fine, but at the end of it, I got
these messages:
java.lang.ArrayIndexOutOfBoundsException: -1
at org.gel.mauve.assembly.AssemblyScorer.computeContigSizeStats(Unknown
Source)
at org.gel.mauve.assembly.AssemblyScorer.loadInfo(Unknown Source)
at org.gel.mauve.assembly.AssemblyScorer.completeAlignment(Unknown
Source)
at org.gel.mauve.contigs.ContigOrderer.fireAlignmentEvent(Unknown
Source)
at org.gel.mauve.contigs.ContigOrderer.reorderDone(Unknown Source)
at org.gel.mauve.contigs.ContigReorderer.initModelData(Unknown Source)
at org.gel.mauve.contigs.ContigReorderer.loadFile(Unknown Source)
at org.gel.mauve.gui.AlignFrame.completeAlignment(Unknown Source)
at org.gel.mauve.gui.AlignWorker.finished(Unknown Source)
at org.gel.mauve.gui.SwingWorker$1.run(Unknown Source)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:312)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:733)
at java.awt.EventQueue.access$200(EventQueue.java:103)
at java.awt.EventQueue$3.run(EventQueue.java:694)
at java.awt.EventQueue$3.run(EventQueue.java:692)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:703)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)
shown
As a result, no assembly scoring files were returned. I only got 2 alignment
folders, each with 9 files inside. However, I had no problem when following the
example on
https://code.google.com/p/ngopt/wiki/How_To_Score_Genome_Assemblies_with_Mauve.
Could you kindly let me know what I got wrong?
I am a real beginner, so please bear with me if I am missing something really
obvious.
Thank you very much.
Best regards,
Raquel
==========================
Raquel Lo
Postdoctoral research fellow
School of Agriculture and Food Sciences
The University of Queensland
St Lucia QLD 4072
Australia
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