Hi Tina, this appears to be a bug in the Mauve snapshot you are using. Would you be able to provide me with a copy of the sequence files & alignment so I can track down the problem and fix it? In the meantime, if you obtain the 2.3.1 release version from here: http://gel.ahabs.wisc.edu/mauve/download.php the problem should (hopefully) not appear because the code in question did not exist in the 2.3.1 release.
Best, -Aaron On Sun, 2014-08-03 at 06:45 +1000, Tina Lan wrote: > Hi, > Can anyone tell me how to fix this error? Below is the error message: > > done. > root alignment has 2 superintervals > root alignment length: 2273551 > Organisms have 42.5% GC > Completed without error. > Alignment complete! > file:/Applications/Mauve/Mauve.app/Contents/Resources/Java/Mauve.jar!/images/Dcj16.gif > 2 LCBs before splitting with getSplitLCBs(XmfaViewerModel). > starting with 1 LCBs > Exception in thread "Thread-14" java.lang.IllegalArgumentException: col > == 83292 : greater than LCB length (length == 5852) > at org.gel.mauve.analysis.PermutationExporter.cropLeft(Unknown Source) > at > org.gel.mauve.analysis.PermutationExporter.splitLCBbyGenome(Unknown Source) > at org.gel.mauve.analysis.PermutationExporter.splitLcbList(Unknown > Source) > at org.gel.mauve.analysis.PermutationExporter.getSplitLCBs(Unknown > Source) > at org.gel.mauve.XmfaViewerModel.init(Unknown Source) > at org.gel.mauve.XmfaViewerModel.<init>(Unknown Source) > at org.gel.mauve.ModelBuilder.buildModel(Unknown Source) > at org.gel.mauve.gui.FrameLoader.loadFile(Unknown Source) > at org.gel.mauve.gui.FrameLoader.run(Unknown Source) > at java.lang.Thread.run(Thread.java:695) > > > Thanks, > Tina > > ------------------------------------------------------------------------------ > Want fast and easy access to all the code in your enterprise? Index and > search up to 200,000 lines of code with a free copy of Black Duck > Code Sight - the same software that powers the world's largest code > search on Ohloh, the Black Duck Open Hub! Try it now. > http://p.sf.net/sfu/bds > _______________________________________________ > 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. ------------------------------------------------------------------------------ _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
