Hi Julie, there seems like there may be a few things going on here. The first issue is that progressiveMauve needs to be added to a directory in $PATH. You or your network admins can do this either by modifying $PATH or by copying the 64-bit progressiveMauve to a directory in $PATH. The headless exception which follows may just be a product of the software trying to pop up a message window to tell you that the alignment failed. If it persists after sorting out your $PATH issue please let me know and we'll dig deeper.
Best, -Aaron On Tue, 2014-10-21 at 09:11 +1100, Julie Shay wrote: > Hi, > I've misplaced the email I received with the response to this, but > it's in the archive from August 15, 2014: > Hi Julie, > I have success with the java 6u45 on ubuntu provided by the webupd8team > ppa. > Best, > -Aaron > A couple of people from my lab, including the systems administrator, > have tried to run the contig mover on headless mode with java 6u45 > from the webupd8team and we are still having problems. I'll copy the > command and errors below. Do you have any more advice to get around > this without an X11 environment? Thanks! > -Julie > > Command and errors: > ./java -Djava.awt.headless=true -Xmx500m > -cp /home/jshay/Programs/mauve/mauve_snapshot_2011-12-16/Mauve.jar > org.gel.mauve.contigs.ContigOrderer -output /home/jshay/mauvetest > -ref /home/jshay/refgenome.gbk -draft /home/jshay/contigs.fasta > ref file: > org.gel.mauve.contigs.ContigMauveAlignFrame[panel0,0,0,343x383,invalid] > shown > Copying... > /home/jshay/refgenome.gbk > to > /home/jshay/mauvetest/alignment1/refgenome.gbk > Copying... > /home/jshay/contigs.fasta > to > /home/jshay/mauvetest/alignment1/contigs.fasta > trying path ./progressiveMauve > Running alignment. > Executing > progressiveMauve > --output=/home/jshay/mauvetest/alignment1/alignment1 > --skip-refinement > --weight=200 > > --output-guide-tree=/home/jshay/mauvetest/alignment1/alignment1.guide_tree > > --backbone-output=/home/jshay/mauvetest/alignment1/alignment1.backbone > /home/jshay/mauvetest/alignment1/refgenome.gbk > /home/jshay/mauvetest/alignment1/contigs.fasta > Error running aligner. > java.io.IOException: Cannot run program "progressiveMauve": > java.io.IOException: error=2, No such file or directory > at java.lang.ProcessBuilder.start(ProcessBuilder.java:470) > at java.lang.Runtime.exec(Runtime.java:593) > at java.lang.Runtime.exec(Runtime.java:466) > at org.gel.mauve.gui.AlignWorker.construct(Unknown Source) > at org.gel.mauve.gui.SwingWorker$2.run(Unknown Source) > at java.lang.Thread.run(Thread.java:662) > Caused by: java.io.IOException: java.io.IOException: error=2, No such > file or directory > at java.lang.UNIXProcess.<init>(UNIXProcess.java:148) > at java.lang.ProcessImpl.start(ProcessImpl.java:65) > at java.lang.ProcessBuilder.start(ProcessBuilder.java:452) > ... 5 more > Exception in thread "AWT-EventQueue-0" java.awt.HeadlessException > at > java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:159) > at java.awt.Window.<init>(Window.java:433) > at java.awt.Frame.<init>(Frame.java:403) > at java.awt.Frame.<init>(Frame.java:368) > at javax.swing.SwingUtilities > $SharedOwnerFrame.<init>(SwingUtilities.java:1733) > at > javax.swing.SwingUtilities.getSharedOwnerFrame(SwingUtilities.java:1810) > at javax.swing.JOptionPane.getRootFrame(JOptionPane.java:1673) > at > javax.swing.JOptionPane.showOptionDialog(JOptionPane.java:846) > at > javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:650) > at > javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:621) > at org.gel.mauve.gui.AlignFrame.completeAlignment(Unknown > Source) > at org.gel.mauve.gui.AlignWorker.finished(Unknown Source) > at org.gel.mauve.gui.SwingWorker$1.run(Unknown Source) > at > java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) > at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:672) > at java.awt.EventQueue.access$400(EventQueue.java:81) > at java.awt.EventQueue$2.run(EventQueue.java:633) > at java.awt.EventQueue$2.run(EventQueue.java:631) > at java.security.AccessController.doPrivileged(Native Method) > at java.security.AccessControlContext > $1.doIntersectionPrivilege(AccessControlContext.java:87) > at java.awt.EventQueue.dispatchEvent(EventQueue.java:642) > at > java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269) > at > java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184) > at > java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174) > at > java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169) > at > java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161) > at > java.awt.EventDispatchThread.run(EventDispatchThread.java:122) > > On 14/08/2014 4:26 PM, Julie Shay wrote: > > > Thanks for replying! I believe we are using Sun JDK. This is what's > > returned when I enter the command "java -version": > > java version "1.7.0_06" > > Java(TM) SE Runtime Environment (build 1.7.0_06-b24) > > Java HotSpot(TM) 64-Bit Server VM (build 23.2-b09, mixed mode) > > > > This is the version I used when I got the errors from my previous > > email. Exactly which version of a Java VM will make this work? Also, > > please let me know if/when there is any development towards fixing > > this problem. Thanks again! > > -Julie > > > > On 12/08/2014 11:00 AM, Aaron Darling wrote: > > > > > Hi Julie, apologies for the delayed response. > > > Matt DeMaere here at UTS has looked into this issue and it appears to be > > > a problem specific to recent versions of OpenJDK. Whereas the code will > > > work command-line on the Sun Java VM without an X11 environment, the > > > OpenJDK implementation of Java library functions used by the contig > > > mover still require an X11 display. We are looking into how this can be > > > fixed. In the meantime it's possible to work around the issue by using a > > > Sun JDK or with the rather hackish approach of creating an X11 > > > environment on the server with, e.g. VNC, that the contig mover can > > > silently connect to. > > > > > > Best, > > > -Aaron > > > > > > On Wed, 2014-07-16 at 06:59 +1000, Julie Shay wrote: > > > > Hi Aaron, > > > > Thanks so much for your quick response. I know that Mauve is great for > > > > genome alignments, and I find the contig mover very useful, which is > > > > why I want to incorporate it into this pipeline. My coworkers and I > > > > have tried to run the contig mover with both the most recent snapshot > > > > and with snapshots shortly following the post I linked below, and we > > > > keep getting similar errors. Here is an example of a command we've > > > > been trying and the errors we've been getting: > > > > > > > > java -Djava.awt.headless=true -Xmx500m > > > > -cp /home/jshay/Programs/mauve/mauve_snapshot_2011-12-16/Mauve.jar > > > > org.gel.mauve.contigs.ContigOrderer -output 0093mauvetest -ref > > > > 0093.gbk -draft 0093spades/contigs.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) > > > > > > > > Do you know of something we might be doing wrong on our end? If we get > > > > this to work, we can use a snapshot and reference the date stamp as > > > > you suggest. Thanks again! > > > > -Julie > > > > > > > > On 13/07/2014 7:43 PM, Aaron Darling wrote: > > > > > > > > > Hi Julie, > > > > > There will be another release with a traditional numeric version > > > > > identifier eventually, but as it currently stands the development > > > > > snapshots are about as "stable" as research software gets. There are a > > > > > number of cosmetic bugs but no major bugs that I am aware of in terms > > > > > of > > > > > the calculation of genome alignments. If you want to incorporate to > > > > > your > > > > > pipeline, I would suggest referencing the datestamp as the software > > > > > version -- the snapshots will remain available to the public so that > > > > > reproducibility of results by others can be achieved by obtaining a > > > > > matching datestamped build of the software. > > > > > > > > > > Best, > > > > > -Aaron > > > > > > > > > > On Fri, 2014-07-11 at 04:32 +1000, Julie Shay wrote: > > > > > > Hi, > > > > > > Are there currently any plans for an official release of a Mauve > > > > > > update? We would like to use the Mauve Contig Mover from the command > > > > > > line on our lab's cluster without an X-display, and I see that > > > > > > you've > > > > > > done an unofficial update that allows this > > > > > > ( http://sourceforge.net/p/mauve/mailman/message/28484265/ ), but I > > > > > > was wondering whether your plans regarding a formal release have > > > > > > changed in the past 2.5 years? We're trying to integrate the Mauve > > > > > > Contig Mover into one of our pipelines, and we want to be confident > > > > > > that the version we use is stable. Thanks! > > > > > > -Julie > > > > > > -- > > Julie Shay > > Graduate Student > > Brinkman Laboratory, MBB Department > > Simon Fraser University, Burnaby, B.C., Canada, V5A 1S6 > > > -- > Julie Shay > Graduate Student > Brinkman Laboratory, MBB Department > Simon Fraser University, Burnaby, B.C., Canada, V5A 1S6 ------------------------------------------------------------------------------ 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
