Hi Oyediran, It looks to me like the directories that Mauve Contig Mover has been asked to use may not exist. Can you check whether $WRKDIR/REFERENCE_GENOME/CAMPY_REF/NCTC11168.gbk
and $WRKDIR/CAMPY/FASTQ_TRIMMED/PAIRED_FASTQ/mygenome_75.final.scaffolds.fasta actually have $WRKDIR set correctly and exist on the system? If they do then there may be a more subtle problem. Best, -Aaron On Wed, 2014-01-29 at 09:47 +0200, Akinrinade, Oyediran O wrote: > Hello! > > > I have been having difficulty using Mauve tool to reorder contigs from > a genome assembly. > > > I have installed Mauve2.3.1 as well as snapshot_2012-06-07 on linux > but couldn’t get either working for the desired task. I am interested > in running it for several assemblies on the command line but its not > just working... > > > Below is a message I got: > > > akinrina@hippu4:/fs/lustre/appl/rhel6/users/akinrina/mauve_snapshot_2012-06-07> > java -cp Mauve.jar org.gel.mauve.contigs.ContigOrderer -output RESULTS -ref > $WRKDIR/REFERENCE_GENOME/CAMPY_REF/NCTC11168.gbk -draft > $WRKDIR/CAMPY/FASTQ_TRIMMED/PAIRED_FASTQ/mygenome_75.final.scaffolds.fasta > Exception in thread "main" java.lang.NullPointerException > at > javax.swing.JFileChooser.isTraversable(JFileChooser.java:1596) > at > javax.swing.JFileChooser.setCurrentDirectory(JFileChooser.java:575) > at javax.swing.JFileChooser.<init>(JFileChooser.java:344) > at javax.swing.JFileChooser.<init>(JFileChooser.java:296) > at org.gel.mauve.gui.AlignFrame$1.<init>(Unknown Source) > at org.gel.mauve.gui.AlignFrame.<init>(Unknown Source) > at org.gel.mauve.gui.ProgressiveMauveAlignFrame.<init>(Unknown > Source) > at org.gel.mauve.contigs.ContigMauveAlignFrame.<init>(Unknown > Source) > at org.gel.mauve.contigs.ContigOrderer.init(Unknown Source) > at org.gel.mauve.contigs.ContigOrderer.<init>(Unknown Source) > at org.gel.mauve.contigs.ContigOrderer.main(Unknown Source) > > > I would appreciate any help from you. > > > Looking forward to hearing from you. > > > BR, > > > -- > Oyediran > ------------------------------------------------------------------------------ > WatchGuard Dimension instantly turns raw network data into actionable > security intelligence. It gives you real-time visual feedback on key > security issues and trends. Skip the complicated setup - simply import > a virtual appliance and go from zero to informed in seconds. > http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk > _______________________________________________ > 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. ------------------------------------------------------------------------------ WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
