Uploaded image for project: 'IGBfx'
  1. IGBfx
  2. IGBFX-105

FileNotFoundException when Tabix-indexer tool is used on Windows

    Details

    • Type: Bug
    • Status: To-Do (View Workflow)
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: IGBfx
    • Labels:
      None

      Description

      System cannot find the specified path to my file when using Tabix-indexer. Getting a FileNotFoundException:

      2016-11-01 10:54:20,119 | ERROR | plication Thread | BedToTabixMenuEntry | 88 - org.lorainelab.igb.filehandler.tabix - 0.0.1 | C:\Users\Wilbur%20Wright\Dropbox\IGB\IGB-testing\Mason's%20Work%20Folder\IGB%20Test%20Files\BED\D_rerio_Jul_2010_refGene.bed (The system cannot find the path specified)
      java.io.FileNotFoundException: C:\Users\Wilbur%20Wright\Dropbox\IGB\IGB-testing\Mason's%20Work%20Folder\IGB%20Test%20Files\BED\D_rerio_Jul_2010_refGene.bed (The system cannot find the path specified)
      at java.io.RandomAccessFile.open0(Native Method)[:1.8.0_77]
      at java.io.RandomAccessFile.open(Unknown Source)[:1.8.0_77]
      at java.io.RandomAccessFile.<init>(Unknown Source)[:1.8.0_77]
      at htsjdk.samtools.seekablestream.SeekableFileStream.<init>(SeekableFileStream.java:47)
      at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:80)
      at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:68)
      at org.lorainelab.igb.filehandler.tabix.BedToTabixWriter.sortedBedToBGzip(BedToTabixWriter.java:34)
      at org.lorainelab.igb.filehandler.tabix.BedToTabixMenuEntry.lambda$initComponents$5(BedToTabixMenuEntry.java:103)
      at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)[jfxrt.jar:]
      at javafx.event.Event.fireEvent(Unknown Source)[jfxrt.jar:]
      at javafx.scene.Node.fireEvent(Unknown Source)[jfxrt.jar:]
      at javafx.scene.control.Button.fire(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.scene.control.skin.BehaviorSkinBase$1.handle(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.scene.control.skin.BehaviorSkinBase$1.handle(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)[jfxrt.jar:]
      at javafx.event.Event.fireEvent(Unknown Source)[jfxrt.jar:]
      at javafx.scene.Scene$MouseHandler.process(Unknown Source)[jfxrt.jar:]
      at javafx.scene.Scene$MouseHandler.access$1500(Unknown Source)[jfxrt.jar:]
      at javafx.scene.Scene.impl_processMouseEvent(Unknown Source)[jfxrt.jar:]
      at javafx.scene.Scene$ScenePeerListener.mouseEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)[jfxrt.jar:]
      at java.security.AccessController.doPrivileged(Native Method)[:1.8.0_77]
      at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$354(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(Unknown Source)[jfxrt.jar:]
      at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.glass.ui.View.handleMouseEvent(Unknown Source)[jfxrt.jar:]
      at com.sun.glass.ui.View.notifyMouse(Unknown Source)[jfxrt.jar:]
      at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)[jfxrt.jar:]
      at com.sun.glass.ui.win.WinApplication.lambda$null$148(Unknown Source)[jfxrt.jar:]
      at java.lang.Thread.run(Unknown Source)[:1.8.0_77]

        Attachments

          Activity

          There are no comments yet on this issue.

            People

            • Assignee:
              dcnorris David Norris (Inactive)
              Reporter:
              mason Mason Meyer (Inactive)
            • Votes:
              0 Vote for this issue
              Watchers:
              1 Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved: