Hi Maryam, This is a clue: > FileNotFoundException: > C:\Users\p270270\Desktop\CompGenTutorial\NC_011748.fna\NC_011748.fna (The > system cannot find the path specified)
When using the GUI interface (on either Windows or MacOS) as opposed to command line, I have discovered that if you double-click on the file name after navigating to it in the interface, the file name is occasionally used as both a directory name and a file name. Single click to select, and then click on the Open button. This happens to me more often with .gbk files, or fasta files with extensions other than .fas or .fasta, so it might reflect some underlying assumption about file names … Any way, try that and see if it solves your issue. Cheers, Guy Dr. Guy Plunkett III Senior Scientist Emeritus, University of Wisconsin-Madison Senior Scientist, DNASTAR, Inc. http://www.genome.wisc.edu/information/gplunkett.html On Oct 5, 2016, at 1:37 AM, Chaib De Mares, M. <m.chaib.de.ma...@rug.nl> wrote: > Hello, > > I am new to this list, and I don't know whether this has been asked before. I > apologize before hand if there's duplication. > When I try to upload my reference and then draft genome to Mauve, I get an > error saying that java cannot bind my document to parent. I am running the > latest JRE version (8u102) on a 64-bit Windows computer. I understand that it > should work, because Mauve can work on 1.4 or later. > Could you please point out what could be the issue? > > See details below: > > Thank you! > Maryam > > ------- > shown > Exception in thread "AWT-EventQueue-0" java.lang.InternalError: Unable to > bind C:\Users\p270270\Desktop\CompGenTutorial\NC_011748.fna to parent > at sun.awt.shell.Win32ShellFolder2$4.call(Unknown Source) > at sun.awt.shell.Win32ShellFolder2$4.call(Unknown Source) > at sun.awt.shell.Win32ShellFolderManager2$ComInvoker.invoke(Unknown > Source) > at sun.awt.shell.ShellFolder.invoke(Unknown Source) > at sun.awt.shell.Win32ShellFolder2.getIShellFolder(Unknown Source) > at sun.awt.shell.Win32ShellFolder2.access$200(Unknown Source) > at sun.awt.shell.Win32ShellFolder2$16.call(Unknown Source) > at sun.awt.shell.Win32ShellFolder2$16.call(Unknown Source) > at java.util.concurrent.FutureTask.run(Unknown Source) > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) > at sun.awt.shell.Win32ShellFolderManager2$ComInvoker$3.run(Unknown Source) > at java.lang.Thread.run(Unknown Source) > Exception in thread "AWT-EventQueue-0" java.lang.InternalError: Unable to > bind C:\Users\p270270\Desktop\CompGenTutorial\SRR292770_unordered.fasta to > parent > at sun.awt.shell.Win32ShellFolder2$4.call(Unknown Source) > at sun.awt.shell.Win32ShellFolder2$4.call(Unknown Source) > at sun.awt.shell.Win32ShellFolderManager2$ComInvoker.invoke(Unknown > Source) > at sun.awt.shell.ShellFolder.invoke(Unknown Source) > at sun.awt.shell.Win32ShellFolder2.getIShellFolder(Unknown Source) > at sun.awt.shell.Win32ShellFolder2.access$200(Unknown Source) > at sun.awt.shell.Win32ShellFolder2$16.call(Unknown Source) > at sun.awt.shell.Win32ShellFolder2$16.call(Unknown Source) > at java.util.concurrent.FutureTask.run(Unknown Source) > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) > at sun.awt.shell.Win32ShellFolderManager2$ComInvoker$3.run(Unknown Source) > at java.lang.Thread.run(Unknown Source) > Copying... > C:\Users\p270270\Desktop\CompGenTutorial\NC_011748.fna\NC_011748.fna > to > > C:\Users\p270270\Desktop\CompGenTutorial\MauveOutput\alignment1\NC_011748.fna > java.io.FileNotFoundException: > C:\Users\p270270\Desktop\CompGenTutorial\NC_011748.fna\NC_011748.fna (The > system cannot find the path specified) > at java.io.FileInputStream.open0(Native Method) > at java.io.FileInputStream.open(Unknown Source) > at java.io.FileInputStream.<init>(Unknown Source) > at org.gel.air.util.IOUtils.copyFile(Unknown Source) > at org.gel.mauve.contigs.ContigOrderer.copyInputFiles(Unknown Source) > at > org.gel.mauve.contigs.ContigMauveAlignFrame.alignButtonActionPerformed(Unknown > Source) > at org.gel.mauve.gui.AlignFrame$9.actionPerformed(Unknown Source) > at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) > at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) > at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) > at javax.swing.DefaultButtonModel.setPressed(Unknown Source) > at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown > Source) > at java.awt.Component.processMouseEvent(Unknown Source) > at javax.swing.JComponent.processMouseEvent(Unknown Source) > at java.awt.Component.processEvent(Unknown Source) > at java.awt.Container.processEvent(Unknown Source) > at java.awt.Component.dispatchEventImpl(Unknown Source) > at java.awt.Container.dispatchEventImpl(Unknown Source) > at java.awt.Component.dispatchEvent(Unknown Source) > at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) > at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) > at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) > at java.awt.Container.dispatchEventImpl(Unknown Source) > at java.awt.Component.dispatchEvent(Unknown Source) > at java.awt.EventQueue.dispatchEventImpl(Unknown Source) > at java.awt.EventQueue.access$500(Unknown Source) > at java.awt.EventQueue$3.run(Unknown Source) > at java.awt.EventQueue$3.run(Unknown Source) > at java.security.AccessController.doPrivileged(Native Method) > at > java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown > Source) > at > java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown > Source) > at java.awt.EventQueue$4.run(Unknown Source) > at java.awt.EventQueue$4.run(Unknown Source) > at java.security.AccessController.doPrivileged(Native Method) > at > java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown > Source) > at java.awt.EventQueue.dispatchEvent(Unknown Source) > at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) > at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) > at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) > at java.awt.EventDispatchThread.pumpEvents(Unknown Source) > at java.awt.EventDispatchThread.pumpEvents(Unknown Source) > at java.awt.EventDispatchThread.run(Unknown Source) > Running alignment. > Executing > win64\progressiveMauve > > --output=C:\Users\p270270\Desktop\CompGenTutorial\MauveOutput\alignment1\alignment1 > --skip-refinement > --weight=200 > > --output-guide-tree=C:\Users\p270270\Desktop\CompGenTutorial\MauveOutput\alignment1\alignment1.guide_tree > > --backbone-output=C:\Users\p270270\Desktop\CompGenTutorial\MauveOutput\alignment1\alignment1.backbone > C:\Users\p270270\Desktop\CompGenTutorial\NC_011748.fna\NC_011748.fna > > C:\Users\p270270\Desktop\CompGenTutorial\SRR292770_unordered.fasta\SRR292770_unordered.fasta > Exception FileNotOpened thrown from > Unknown() in ..\libGenome\gnFileSource.cpp 67 > Called by Unknown() > Exited with error code: -1073741676 > -- > Maryam Chaib De Mares > M.Sc. Evolutionary Biology > PhD Candidate - Microbial Ecology Department > Groningen Institute for Evolutionary Life Sciences (GELIFES) > Rijksuniversiteit Groningen > Nijenborgh 7, 9747 AG Groningen > Linnaeusborg, room 0766 > +31 50 363 2169 > m.chaib.de.ma...@rug.nl > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! > http://sdm.link/slashdot_______________________________________________ > Mauve-users mailing list > Mauve-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mauve-users
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