Hi Fatma, This looks like an off-by-one bug somewhere in the aligner or GUI. It would be easiest for me to track down and fix if you could provide the alignment and input sequence files you are using. Obviously they are far too big for email attachments so perhaps you could use a cloud storage service (dropbox?) to share them with me privately?
Best, -Aaron On Tue, 2014-05-06 at 03:15 +1000, Fatma Onmus wrote: > Hello All, > > We are now using snapshot-2012-06-07 for SNP export per Aaron's > suggestion. We run this on Linux. We successfully exported the SNP > file before so we decided to accelarate a bit and ran 60 genomes.The > backbone file(.xmfa) was created with no problem. However SNP export > failed due to ArrayIndexOutOfBoundsException error. Please see below: > > "java.lang.ArrayIndexOutOfBoundsException: genome 1656-2.fna position > 3940615 > at org.gel.mauveXMFAAlignment.getLCB(unknown Source) > at org.gel.mauveXMFAViewerModel.getLCBIndex(unknown source) > at org.gel.mauve.analysis.SnpExporter.getSNPs(unknown source) > at org.gel.mauve.analysis.SnpExporter.getSNPs(unknown source) > at org.gel.mauve.analysis.SnpExporter.exporter(unknown source) > at org.gel.mauve.analysis.SnpExporter.main (unknown source)" > > It seems like the last coordinate in xmfa file for Acinetobacter > baumannii 1656-2 is 1:3911977-3940614. I am not sure where 3940615 > comes from and how to correct this errror. > > Thank you so much for your time in advance! > Fatma -- 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. ------------------------------------------------------------------------------ Is your legacy SCM system holding you back? Join Perforce May 7 to find out: • 3 signs your SCM is hindering your productivity • Requirements for releasing software faster • Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
