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  1. Deep Backlog
  2. DB-96

"Out of Memory Error" when loading sequence for Macaca mulatta genome

    Details

    • Type: Bug
    • Status: Open (View Workflow)
    • Priority: Major
    • Resolution: Unresolved
    • Labels:
      None

      Description

      While testing I noticed that I could not load the sequence for the Macaca mulatta genome. Instead an "Execution exception" occurred in which there was an "out of memory error".

      *I noticed this on my office Mac:
      -(My Office Mac) Mac OS X Version 10.9.3 using JRE version 1.8.0_11-b12 Java HotSpot(TM) 64-Bit Server

      To Reproduce:
      1) Open the most recent version of the Macaca mulatta genome.
      2) Select "refGene" from the Available Data pane and load the data.
      3) Now try to load the sequence...

      Observe:
      The status bar indicates that IGB continuously loads and eventually you will see an exception in the console (see next comment for console exception).

        Attachments

          Activity

          mason Mason Meyer (Inactive) created issue -
          Hide
          mason Mason Meyer (Inactive) added a comment -

          java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: Java heap space
          at java.util.concurrent.FutureTask.report(FutureTask.java:122)
          at java.util.concurrent.FutureTask.get(FutureTask.java:192)
          at javax.swing.SwingWorker.get(SwingWorker.java:602)
          at com.affymetrix.igb.view.load.GeneralLoadView$1.finished(GeneralLoadView.java:150)
          at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:47)
          at javax.swing.SwingWorker$5.run(SwingWorker.java:737)
          at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:832)
          at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:112)
          at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:842)
          at javax.swing.Timer.fireActionPerformed(Timer.java:313)
          at javax.swing.Timer$DoPostEvent.run(Timer.java:245)
          at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
          at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:744)
          at java.awt.EventQueue.access$400(EventQueue.java:97)
          at java.awt.EventQueue$3.run(EventQueue.java:697)
          at java.awt.EventQueue$3.run(EventQueue.java:691)
          at java.security.AccessController.doPrivileged(Native Method)
          at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
          at java.awt.EventQueue.dispatchEvent(EventQueue.java:714)
          at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
          at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
          at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
          at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
          at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
          Caused by: java.lang.OutOfMemoryError: Java heap space
          at java.util.Arrays.copyOf(Arrays.java:3326)
          at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:137)
          at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:121)
          at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:514)
          at java.lang.StringBuffer.append(StringBuffer.java:352)
          at java.util.regex.Matcher.appendReplacement(Matcher.java:888)
          at java.util.regex.Matcher.replaceAll(Matcher.java:955)
          at com.affymetrix.genometryImpl.das.DasResiduesHandler.endElement(DasResiduesHandler.java:111)
          at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:609)
          at com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.endNamespaceScope(XMLDTDValidator.java:2054)
          at com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.handleEndElement(XMLDTDValidator.java:2005)
          at com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.endElement(XMLDTDValidator.java:879)
          at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:1782)
          at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2973)
          at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:606)
          at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510)
          at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:848)
          at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:777)
          at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
          at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213)
          at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:649)
          at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(SAXParserImpl.java:333)
          at javax.xml.parsers.SAXParser.parse(SAXParser.java:195)
          at com.affymetrix.genometryImpl.das.DasResiduesHandler.getDasResidues(DasResiduesHandler.java:54)
          at com.affymetrix.genometryImpl.das.DasServerType.getResidues(DasServerType.java:375)
          at com.affymetrix.igb.view.load.GeneralLoadUtils.getResidues(GeneralLoadUtils.java:1057)
          at com.affymetrix.igb.view.load.GeneralLoadUtils.loadResidues(GeneralLoadUtils.java:1105)
          at com.affymetrix.igb.view.load.GeneralLoadView.loadResidues(GeneralLoadView.java:177)
          at com.affymetrix.igb.view.load.GeneralLoadView.access$100(GeneralLoadView.java:62)
          at com.affymetrix.igb.view.load.GeneralLoadView$1.runInBackground(GeneralLoadView.java:144)
          at com.affymetrix.igb.view.load.GeneralLoadView$1.runInBackground(GeneralLoadView.java:141)
          at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:69)

          Show
          mason Mason Meyer (Inactive) added a comment - java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: Java heap space at java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.util.concurrent.FutureTask.get(FutureTask.java:192) at javax.swing.SwingWorker.get(SwingWorker.java:602) at com.affymetrix.igb.view.load.GeneralLoadView$1.finished(GeneralLoadView.java:150) at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:47) at javax.swing.SwingWorker$5.run(SwingWorker.java:737) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:832) at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:112) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:842) at javax.swing.Timer.fireActionPerformed(Timer.java:313) at javax.swing.Timer$DoPostEvent.run(Timer.java:245) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:744) at java.awt.EventQueue.access$400(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:697) at java.awt.EventQueue$3.run(EventQueue.java:691) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) at java.awt.EventQueue.dispatchEvent(EventQueue.java:714) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: java.lang.OutOfMemoryError: Java heap space at java.util.Arrays.copyOf(Arrays.java:3326) at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:137) at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:121) at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:514) at java.lang.StringBuffer.append(StringBuffer.java:352) at java.util.regex.Matcher.appendReplacement(Matcher.java:888) at java.util.regex.Matcher.replaceAll(Matcher.java:955) at com.affymetrix.genometryImpl.das.DasResiduesHandler.endElement(DasResiduesHandler.java:111) at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:609) at com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.endNamespaceScope(XMLDTDValidator.java:2054) at com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.handleEndElement(XMLDTDValidator.java:2005) at com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.endElement(XMLDTDValidator.java:879) at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:1782) at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2973) at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:606) at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510) at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:848) at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:777) at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141) at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213) at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:649) at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(SAXParserImpl.java:333) at javax.xml.parsers.SAXParser.parse(SAXParser.java:195) at com.affymetrix.genometryImpl.das.DasResiduesHandler.getDasResidues(DasResiduesHandler.java:54) at com.affymetrix.genometryImpl.das.DasServerType.getResidues(DasServerType.java:375) at com.affymetrix.igb.view.load.GeneralLoadUtils.getResidues(GeneralLoadUtils.java:1057) at com.affymetrix.igb.view.load.GeneralLoadUtils.loadResidues(GeneralLoadUtils.java:1105) at com.affymetrix.igb.view.load.GeneralLoadView.loadResidues(GeneralLoadView.java:177) at com.affymetrix.igb.view.load.GeneralLoadView.access$100(GeneralLoadView.java:62) at com.affymetrix.igb.view.load.GeneralLoadView$1.runInBackground(GeneralLoadView.java:144) at com.affymetrix.igb.view.load.GeneralLoadView$1.runInBackground(GeneralLoadView.java:141) at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:69)
          dcnorris David Norris (Inactive) made changes -
          Field Original Value New Value
          Rank Ranked lower
          mason Mason Meyer (Inactive) made changes -
          Epic Link IGBF-497 [ 15559 ]
          mason Mason Meyer (Inactive) made changes -
          Rank Ranked lower
          mason Mason Meyer (Inactive) made changes -
          Rank Ranked higher
          mason Mason Meyer (Inactive) made changes -
          Rank Ranked higher
          mason Mason Meyer (Inactive) made changes -
          Project IGB [ 10840 ] Deep Backlog [ 11041 ]
          Key IGBF-163 DB-96
          Workflow Loraine Lab Workflow [ 14804 ] jira [ 16803 ]

            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: