Hi Tom, can you send any additional details about the error? The console log available from the help menu is often much more informative about the reason for an alignment failure than the numeric error code.
One possible reason that progressiveMauve did not work is that it simply did not have enough RAM to complete the alignment. progressiveMauve can be quite memory-hungry, especially when the genomes are heavily rearranged. If your genomes are draft assemblies and it is possible to reorder them relative to a reference genome prior to alignment I would suggest doing so (using the Mauve Contig Mover command-line or another tool) prior to progressiveMauve alignment. mauveAligner is only aligning the core genome, whereas progressiveMauve will align all positional homologs, even if they're not part of the core, and generally does more accurate core genome alignment as well. If you're only interested in the core genome you might look at the new Harvest tools for highly scalable core genome alignment: https://github.com/marbl/harvest Best, -Aaron On Tue, 2014-10-14 at 00:31 +1100, Tom Geissmann wrote: > Hi, > > I've 42 bacterial genomes to align. I use a MacPro intel xeon E5 with 32 Go > RAM. When I'm using progressiveMauve it exits with an error code 134 after a > while. When I'm using the older MauveAligner algorithm, the job is processed > and the alignement looks OK. I'm wondering about the differences of the two > algorithms? And why progressiveMauve exits with an error > > Thanks for any explanations, > > Tom > > > > Tom Geissmann > tom.geissm...@inserm.fr > > > > > ------------------------------------------------------------------------------ > 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
