Yes, it did. Thank you very much!
On Wed, Oct 5, 2016 at 2:57 PM, Guy Plunkett III <guy.plunk...@wisc.edu>
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.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______
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>
>
>
--
--
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
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