Details
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Type: Bug
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Status: To-Do (View Workflow)
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Priority: Major
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: IGBfx
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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
Field | Original Value | New Value |
---|---|---|
Workflow | Loraine Lab Workflow [ 17632 ] | Fall 2019 Workflow Update [ 20366 ] |
Workflow | Fall 2019 Workflow Update [ 20366 ] | Revised Fall 2019 Workflow Update [ 22586 ] |
Status | Open [ 1 ] | To-Do [ 10305 ] |