Details

    • Type: Bug
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Fixed
    • Labels:
      None

      Description

      1. Create a new folder and named it "untitled folder"(need space in the middle)
      2. Move any VCF files to the folder
      3. Drag the VCF files to IGB

      Error in console:
      java.io.FileNotFoundException: /Users/admin/Desktop/data/vcf/untitled%20folder/ALL.chr20.vqsr_2of5_union_200_sites_for_validation.20101123.indels.genotypes.vcf.gz.tbi (No such file or directory)
      at java.io.FileInputStream.open(Native Method)
      at java.io.FileInputStream.<init>(FileInputStream.java:106)
      at org.broad.tribble.util.SeekableFileStream.<init>(SeekableFileStream.java:50)
      at org.broad.tribble.util.BlockCompressedInputStream.<init>(BlockCompressedInputStream.java:69)
      at com.affymetrix.genometryImpl.symloader.SymLoaderTabix.isTabix(SymLoaderTabix.java:163)
      at com.gene.vcfhandler.VCFHandler.createSymLoader(Unknown Source)
      at com.affymetrix.genometryImpl.util.ServerUtils.determineLoader(ServerUtils.java:1098)
      at com.affymetrix.igb.view.load.GeneralLoadUtils.getFeature(GeneralLoadUtils.java:1259)
      at com.affymetrix.igb.view.load.GeneralLoadUtils.openURI(GeneralLoadUtils.java:1154)
      at com.affymetrix.igb.IGBServiceImpl.openURI(IGBServiceImpl.java:381)
      at com.affymetrix.igb.shared.OpenURIAction.openURI(OpenURIAction.java:48)
      at com.affymetrix.igb.shared.OpenURIAction.openURI(OpenURIAction.java:74)
      at com.affymetrix.igb.action.LoadFileAction.access$000(LoadFileAction.java:34)
      at com.affymetrix.igb.action.LoadFileAction$1.openFileAction(LoadFileAction.java:50)
      at com.affymetrix.genometryImpl.util.FileDropHandler.importData(FileDropHandler.java:40)
      at javax.swing.TransferHandler$DropHandler.drop(TransferHandler.java:1478)
      at java.awt.dnd.DropTarget.drop(DropTarget.java:434)
      at javax.swing.TransferHandler$SwingDropTarget.drop(TransferHandler.java:1203)
      at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:519)
      at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:832)
      at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:756)
      at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:30)
      at java.awt.Component.dispatchEventImpl(Component.java:4593)
      at java.awt.Container.dispatchEventImpl(Container.java:2143)
      at java.awt.Window.dispatchEventImpl(Window.java:2478)
      at java.awt.Component.dispatchEvent(Component.java:4566)
      at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:680)
      at java.awt.EventQueue.access$000(EventQueue.java:86)
      at java.awt.EventQueue$1.run(EventQueue.java:639)
      at java.awt.EventQueue$1.run(EventQueue.java:637)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
      at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
      at java.awt.EventQueue$2.run(EventQueue.java:653)
      at java.awt.EventQueue$2.run(EventQueue.java:651)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
      at java.awt.EventQueue.dispatchEvent(EventQueue.java:650)
      at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
      at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
      at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
      at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
      at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
      at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

      I think the problem is IGB converting " " to 20% somewhere...

      Hiral said probably Big Bed and Big Wig have the same problem.

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            Hide
            richard Richard Linchangco (Inactive) added a comment -

            Passed V.13655, Mac, Java 1.06.0_37

            Tested with .vcf file:

            by downloading to Desktop and putting in a folder titled 'untitled folder' WITH a space between untitled and folder.

            Show
            richard Richard Linchangco (Inactive) added a comment - Passed V.13655, Mac, Java 1.06.0_37 Tested with .vcf file: http://bioviz.org/filerepo/vcf/ALL.chr20.vqsr_2of5_union_200_sites_for_validation.20101123.indels.genotypes.vcf.gz by downloading to Desktop and putting in a folder titled 'untitled folder' WITH a space between untitled and folder.
            Hide
            richard Richard Linchangco (Inactive) added a comment -

            Passed V.13526, Mac, Java 1.06.0_37

            Tested .vcf, .bigwig, .bb, .wig files

            Show
            richard Richard Linchangco (Inactive) added a comment - Passed V.13526, Mac, Java 1.06.0_37 Tested .vcf, .bigwig, .bb, .wig files
            Hide
            fwang4 Fuquan Wang (Inactive) added a comment - - edited

            Passed on 7.0.0 (11945) Mac.

            Show
            fwang4 Fuquan Wang (Inactive) added a comment - - edited Passed on 7.0.0 (11945) Mac.
            Hide
            imnick Nick Ren (Inactive) added a comment -

            Fixed in version 10196.

            Show
            imnick Nick Ren (Inactive) added a comment - Fixed in version 10196.

              People

              • Assignee:
                Unassigned
                Reporter:
                imnick Nick Ren (Inactive)
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                Dates

                • Created:
                  Updated:
                  Resolved: