Hello Hiren, On Wed, 2014-06-04 at 15:02 +0200, Hiren Ghosh wrote: > Hello all i was trying to run mauve as a batch mode in such a way > > > for draft in *.fasta > do > echo $draft > #$ref= Ecoli_jj1886_complete_geneone.fasta; > $bname=echo $draft > > java -Xmx500m -cp Mauve.jar org.gel.mauve.contigs.ContigOrderer > -output $bname -ref ref.fasta -draft $draft > > done > > > > But some error is coming can anyone suggest me what is the problem??? > and can any one please include how i can put number of threads in > command line ???
It might help if you can actually tell us what the error message is. Since I have to guess, it's probably an issue with the program running on a server where an X11 display is not available. If you want to run the contig orderer on a remote server you'll need to get the latest snapshot: http://gel.ahabs.wisc.edu/mauve/snapshots which should operate in a headless environment. if the problem persists please write back and include the error message. -Aaron -- 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. ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
