Details
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Type: Bug
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Status: Open (View Workflow)
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Priority: Major
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Resolution: Unresolved
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Labels:None
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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).
Attachments
Activity
Mason Meyer (Inactive)
created issue -
David Norris (Inactive)
made changes -
Field | Original Value | New Value |
---|---|---|
Rank | Ranked lower |
Mason Meyer (Inactive)
made changes -
Epic Link | IGBF-497 [ 15559 ] |
Mason Meyer (Inactive)
made changes -
Rank | Ranked lower |
Mason Meyer (Inactive)
made changes -
Rank | Ranked higher |
Mason Meyer (Inactive)
made changes -
Rank | Ranked higher |
Mason Meyer (Inactive)
made changes -
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)