Details
-
Type:
Bug
-
Status: Open (View Workflow)
-
Priority:
Major
-
Resolution: Unresolved
-
Labels:None
-
Epic Link:
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).
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)