Hi Raquel, I've not observed this bug in the past. Would it be possible for you to share the input files on which you observe this behavior (off-list)? One possibility is that BioJava is unable to parse one of the sequence files you are using, but it's not clear whether it's that or another problem from the stack trace you've sent. If you can't send the files themselves, at least having the rest of the console output and command-line you used may provide additional clues as to what went wrong.
Cheers, -Aaron On Wed, 2014-10-15 at 16:02 +1100, Raquel Lo wrote: > 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 > ------------------------------------------------------------------------------ > Comprehensive Server Monitoring with Site24x7. > Monitor 10 servers for $9/Month. > Get alerted through email, SMS, voice calls or mobile push notifications. > Take corrective actions from your mobile device. > http://p.sf.net/sfu/Zoho > _______________________________________________ > Mauve-users mailing list > Mauve-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mauve-users -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. ------------------------------------------------------------------------------ Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
