Hi Sarah, On Tue, 2009-10-06 at 17:24 -0400, Sarah Munro wrote: > Hi, > I'm a new user of Mauve 2.3.0, it's really useful, but I'm having a > problem with the Export Orthologs function. I have an alignment with > two closely related genomes, the SNPs export works fine but the > orthologs export just creates an empty file. Can anyone give me > suggestions of how to fix this problem?
This error happens when one attempts to export orthologs based on a genome alignment computed by the mauveAligner algorithm. Ortholog export currently only works for alignments computed with progressiveMauve. So to get the ortholog export working, just realign the genomes using the "Align with progressiveMauve..." menu option. The next release of Mauve will handle this situation better than the current version; either by disabling the export orthologs option for mauveAligner-created alignments or with a more informative error message. In addition to the main error, it looks like your GenBank annotated files may have some sequence coordinates in a format that BioJava does not like. That may cause a few annotations to go missing in the Mauve viewer. Hope that helps, -Aaron > The message I get in the mauve console window is this : > > From must be less than To: /function=" > From must be less than To: /function=" > From must be less than To: /function=" > >From must be less than To: /function=" > From must be less than To: /function=" > From must be less than To: /function=" > From must be less than To: /function=" > >From must be less than To: /function=" > From must be less than To: /function=" > From must be less than To: /function=" > From must be less than To: /function=" > >From must be less than To: /function=" > From must be less than To: /function=" > From must be less than To: /function=" > From must be less than To: /function=" > >From must be less than To: /function=" > From must be less than To: /function=" > From must be less than To: /function=" > From must be less than To: /function=" > >From must be less than To: /function=" > Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException > at > org.gel.mauve.analysis.OneToOneOrthologExporter.getBackboneSegs(Unknown > Source) > at org.gel.mauve.analysis.OneToOneOrthologExporter.export(Unknown > Source) > at org.gel.mauve.analysis.OneToOneOrthologExporter > $ExportFrame.doExport(Unknown Source) > at org.gel.mauve.analysis.OneToOneOrthologExporter > $ExportFrame.access$200(Unknown Source) > at org.gel.mauve.analysis.OneToOneOrthologExporter$ExportFrame > $2.actionPerformed(Unknown Source) > at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) > at javax.swing.AbstractButton$Handler.actionPerformed(Unknown > Source) > at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown > Source) > at javax.swing.DefaultButtonModel.setPressed(Unknown Source) > at > javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown > Source) > at java.awt.Component.processMouseEvent(Unknown Source) > at javax.swing.JComponent.processMouseEvent(Unknown Source) > at java.awt.Component.processEvent(Unknown Source) > at java.awt.Container.processEvent(Unknown Source) > at java.awt.Component.dispatchEventImpl(Unknown Source) > at java.awt.Container.dispatchEventImpl(Unknown Source) > at java.awt.Component.dispatchEvent(Unknown Source) > at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown > Source) > at java.awt.LightweightDispatcher.processMouseEvent(Unknown > Source) > at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) > at java.awt.Container.dispatchEventImpl(Unknown Source) > at java.awt.Window.dispatchEventImpl(Unknown Source) > at java.awt.Component.dispatchEvent(Unknown Source) > at java.awt.EventQueue.dispatchEvent(Unknown Source) > at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown > Source) > at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown > Source) > at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown > Source) > at java.awt.EventDispatchThread.pumpEvents(Unknown Source) > at java.awt.EventDispatchThread.pumpEvents(Unknown Source) > at java.awt.EventDispatchThread.run(Unknown Source) > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ Mauve-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/mauve-users ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
