Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-522

Saving a track as a Bed-detail file generates an exception

        Details

        • Type: Bug
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          An exception is generated when using IGB's "Save Track As..." feature.

          To reproduce:
          1) Open the A. thaliana genome and use the "Save Track As..." option in the context menu to save a "bed-detail" file. (Must change drop-down box for file type)

          *Observe:
          An exception is generated:

          15:28:40.285 ERROR c.a.g.parsers.BedDetailWriter - Stream Closed
          java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.symmetry.impl.UcscBedSym.outputBedFormat(UcscBedSym.java:229) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.symmetry.impl.UcscBedDetailSym.outputBedDetailFormat(UcscBedDetailSym.java:57) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeSymmetry(BedDetailWriter.java:56) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:36) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.igb.action.ExportFileAction.exportFile(ExportFileAction.java:60) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.saveAsFile(AbstractExportFileAction.java:115) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.actionPerformed(AbstractExportFileAction.java:79) [igb-8.4.0.jar:na]
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at javax.swing.JComponent.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Window.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.access$500(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.run(Unknown Source) [na:1.8.0_40]
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.close(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:40) ~[genometry-8.4.0.jar:na]
          ... 42 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.write(Unknown Source)
          at java.io.DataOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 44 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.DataOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 45 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 46 common frames omitted
          15:28:40.289 ERROR c.a.g.parsers.BedDetailWriter - Stream Closed
          java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeSymmetry(BedDetailWriter.java:57) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:36) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.igb.action.ExportFileAction.exportFile(ExportFileAction.java:60) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.saveAsFile(AbstractExportFileAction.java:115) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.actionPerformed(AbstractExportFileAction.java:79) [igb-8.4.0.jar:na]
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at javax.swing.JComponent.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Window.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.access$500(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.run(Unknown Source) [na:1.8.0_40]
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.close(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:40) ~[genometry-8.4.0.jar:na]
          ... 42 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.write(Unknown Source)
          at java.io.DataOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 44 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.DataOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 45 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 46 common frames omitted
          15:28:40.291 ERROR c.a.g.parsers.BedDetailWriter - Stream Closed
          java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.symmetry.impl.UcscBedSym.outputBedFormat(UcscBedSym.java:268) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.symmetry.impl.UcscBedDetailSym.outputBedDetailFormat(UcscBedDetailSym.java:57) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeSymmetry(BedDetailWriter.java:56) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:36) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.igb.action.ExportFileAction.exportFile(ExportFileAction.java:60) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.saveAsFile(AbstractExportFileAction.java:115) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.actionPerformed(AbstractExportFileAction.java:79) [igb-8.4.0.jar:na]
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at javax.swing.JComponent.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Window.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.access$500(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.run(Unknown Source) [na:1.8.0_40]
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.close(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:40) ~[genometry-8.4.0.jar:na]
          ... 42 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.write(Unknown Source)
          at java.io.DataOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 44 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.DataOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 45 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 46 common frames omitted
          15:28:40.295 ERROR c.a.g.parsers.BedDetailWriter - Stream Closed
          java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.symmetry.impl.UcscBedSym.outputBedFormat(UcscBedSym.java:269) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.symmetry.impl.UcscBedDetailSym.outputBedDetailFormat(UcscBedDetailSym.java:57) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeSymmetry(BedDetailWriter.java:56) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:36) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.igb.action.ExportFileAction.exportFile(ExportFileAction.java:60) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.saveAsFile(AbstractExportFileAction.java:115) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.actionPerformed(AbstractExportFileAction.java:79) [igb-8.4.0.jar:na]
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at javax.swing.JComponent.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Window.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.access$500(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.run(Unknown Source) [na:1.8.0_40]
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.close(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:40) ~[genometry-8.4.0.jar:na]
          ... 42 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.write(Unknown Source)
          at java.io.DataOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 44 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.DataOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 45 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 46 common frames omitted
          15:28:40.296 ERROR c.a.g.parsers.BedDetailWriter - Stream Closed
          java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.symmetry.impl.UcscBedDetailSym.outputBedDetailFormat(UcscBedDetailSym.java:59) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeSymmetry(BedDetailWriter.java:56) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:36) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.igb.action.ExportFileAction.exportFile(ExportFileAction.java:60) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.saveAsFile(AbstractExportFileAction.java:115) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.actionPerformed(AbstractExportFileAction.java:79) [igb-8.4.0.jar:na]
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at javax.swing.JComponent.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Window.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.access$500(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.run(Unknown Source) [na:1.8.0_40]
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.close(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:40) ~[genometry-8.4.0.jar:na]
          ... 42 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.write(Unknown Source)
          at java.io.DataOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 44 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.DataOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 45 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 46 common frames omitted
          15:28:40.298 ERROR c.a.g.parsers.BedDetailWriter - Stream Closed
          java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.symmetry.impl.UcscBedSym.outputBedFormat(UcscBedSym.java:227) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.symmetry.impl.UcscBedDetailSym.outputBedDetailFormat(UcscBedDetailSym.java:57) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeSymmetry(BedDetailWriter.java:56) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:36) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.igb.action.ExportFileAction.exportFile(ExportFileAction.java:60) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.saveAsFile(AbstractExportFileAction.java:115) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.actionPerformed(AbstractExportFileAction.java:79) [igb-8.4.0.jar:na]
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at javax.swing.JComponent.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Window.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.access$500(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.run(Unknown Source) [na:1.8.0_40]
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.close(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.parsers.BedDetailWriter.writeAnnotations(BedDetailWriter.java:40) ~[genometry-8.4.0.jar:na]
          ... 42 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.write(Unknown Source)
          at java.io.DataOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 44 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.DataOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 45 common frames omitted
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method)
          at java.io.FileOutputStream.write(Unknown Source)
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
          at java.io.BufferedOutputStream.flush(Unknown Source)
          at java.io.FilterOutputStream.close(Unknown Source)
          ... 46 common frames omitted
          15:28:40.299 ERROR c.a.genometry.util.GeneralUtils - null
          java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.DataOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.close(Unknown Source) ~[na:1.8.0_40]
          at com.affymetrix.genometry.util.GeneralUtils.safeClose(GeneralUtils.java:72) ~[genometry-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.saveAsFile(AbstractExportFileAction.java:119) [igb-8.4.0.jar:na]
          at com.affymetrix.igb.action.AbstractExportFileAction.actionPerformed(AbstractExportFileAction.java:79) [igb-8.4.0.jar:na]
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) [na:1.8.0_40]
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source) [na:1.8.0_40]
          at javax.swing.AbstractButton.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) [na:1.8.0_40]
          at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at javax.swing.JComponent.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.processEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Window.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.access$500(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
          at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
          at java.awt.EventQueue.dispatchEvent(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
          at java.awt.EventDispatchThread.run(Unknown Source) [na:1.8.0_40]
          Suppressed: java.io.IOException: Stream Closed
          at java.io.FileOutputStream.writeBytes(Native Method) ~[na:1.8.0_40]
          at java.io.FileOutputStream.write(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flushBuffer(Unknown Source) ~[na:1.8.0_40]
          at java.io.BufferedOutputStream.flush(Unknown Source) ~[na:1.8.0_40]
          at java.io.FilterOutputStream.close(Unknown Source) ~[na:1.8.0_40]
          ... 43 common frames omitted

            Attachments

              Activity

              Ascending order - Click to sort in descending order
              mason Mason Meyer (Inactive) created issue -
              mason Mason Meyer (Inactive) made changes -
              Field Original Value New Value
              Epic Link IGBF-439 [ 15497 ]
              dcnorris David Norris (Inactive) made changes -
              Assignee David Norris [ dcnorris ]
              dcnorris David Norris (Inactive) made changes -
              Status Open [ 1 ] Needs Testing [ 10002 ]
              dcnorris David Norris (Inactive) made changes -
              Sprint Sprint 16 [ 21 ]
              dcnorris David Norris (Inactive) made changes -
              Rank Ranked higher
              dcnorris David Norris (Inactive) made changes -
              Story Points 0.265
              dcnorris David Norris (Inactive) made changes -
              Story Points 0.265 0.25
              mason Mason Meyer (Inactive) made changes -
              Resolution Done [ 10000 ]
              Status Needs Testing [ 10002 ] Closed [ 6 ]
              ann.loraine Ann Loraine made changes -
              Workflow Loraine Lab Workflow [ 15788 ] Fall 2019 Workflow Update [ 19427 ]
              ann.loraine Ann Loraine made changes -
              Workflow Fall 2019 Workflow Update [ 19427 ] Revised Fall 2019 Workflow Update [ 21544 ]

                People

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

                  Dates

                  • Created:
                    Updated:
                    Resolved: