Hi Jonas, this is an issue that's specific to the Java VM that you're using. I just wrote a separate message about it but the short story workaround is that if you can switch to the Sun VM the problem should go away.
On Wed, 2014-06-25 at 00:57 +1000, Jonas Torgny Larsson wrote: > Dear all, > > I have a problem when trying to run ContigOrderer from command line. It works > fine from the GUI but I get some errors in the shell. > > java -Xmx500m -cp /home/jlr/Build/mauve_snapshot_2012-06-07/Mauve.jar > org.gel.mauve.contigs.ContigOrderer -output test -ref NC_003210.fna -draft > 42-40_20071307_clc.fa > 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 have tried it with absolute paths as well, but the same error comes up. I > have tried adding /home/jlr/Build/mauve_snapshot_2012-06-07/ to my PATH. The > error have been up in the list previously but then I never saw the final > solution. It just looks like the paths to my files and/or directories are > wrong, but I have no real idea how to fix it. > > Best wishes, Jonas > > ________________________________ > > STATENS SERUM INSTITUT > 5 Artillerivej | DK-2300 Copenhagen S | T +45 3268 3268 | F +45 3268 3868 | E > se...@ssi.dk<mailto:se...@ssi.dk> | W ssi.dk<http://www.ssi.dk> > > ________________________________ > > This e-mail, inclusive of attachments, is intended for the person(s) or > entity stated above and may contain confidential information. Unauthorised > reading, disclosure, copying, distribution or use of this information may > violate rights to proprietary information. If you are not an intended > recipient, please return this e-mail to the sender and delete your copy. > Thank you. > > ------------------------------------------------------------------------------ > Open source business process management suite built on Java and Eclipse > Turn processes into business applications with Bonita BPM Community Edition > Quickly connect people, data, and systems into organized workflows > Winner of BOSSIE, CODIE, OW2 and Gartner awards > http://p.sf.net/sfu/Bonitasoft > _______________________________________________ > 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
