Hi Everybody,
Here is the command I am using to run Mauve
(mauve_linux_snapshot_2011-07-18)
java -cp Mauve.jar org.gel.mauve.assembly.ScoreAssembly -reference ref.gbk
-assembly file.fas -reorder -outputDir odir
The run crashes with java.lang.ArrayIndexOutOfBoundsException (full err
below) in some cases. Can this be due to the assembly being longer than the
reference genome? However, I have been able to run Mauve successfully on
longer assemblies with the same installation.
Thanks
-Surya
java.lang.ArrayIndexOutOfBoundsException: genome Genome1 position 6145943
at org.gel.mauve.XMFAAlignment.getLCB(Unknown Source)
at org.gel.mauve.XMFAAlignment.getRange(Unknown Source)
at org.gel.mauve.XmfaViewerModel.getSequenceRange(Unknown Source)
at org.gel.mauve.XmfaViewerModel.getSequenceRange(Unknown Source)
at org.gel.mauve.assembly.AssemblyScorer.printMissingRegions(Unknown
Source)
at org.gel.mauve.assembly.AssemblyScorer.printInfo(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:226)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:647)
at java.awt.EventQueue.access$000(EventQueue.java:96)
at java.awt.EventQueue$1.run(EventQueue.java:608)
at java.awt.EventQueue$1.run(EventQueue.java:606)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:105)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:617)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:275)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:200)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:185)
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:177)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:138)
------------------------------------------------------------------------------
Special Offer -- Download ArcSight Logger for FREE!
Finally, a world-class log management solution at an even better
price-free! And you'll get a free "Love Thy Logs" t-shirt when you
download Logger. Secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsisghtdev2dev
_______________________________________________
Mauve-users mailing list
Mauve-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mauve-users
