Re: [Mauve-users] Cannot bind file to parent
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From: Chaib De M. M. <m.c...@ru...> - 2016-10-05 13:02:34
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Yes, it did. Thank you very much! On Wed, Oct 5, 2016 at 2:57 PM, Guy Plunkett III <guy...@wi...> wrote: > 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.c...@ru...> > 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.c...@ru... > ------------------------------------------------------------ > ------------------ > 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 > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users > > > -- -- 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.c...@ru... |