Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Fixed
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Labels:None
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Environment:
Mac
Description
When I tried to load a session which had one bed file, one bam file and on e wig file and 6 tracks the following exception occurred on the console and IGB got hanged up
java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: Java heap space
at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222)
at java.util.concurrent.FutureTask.get(FutureTask.java:83)
at javax.swing.SwingWorker.get(SwingWorker.java:582)
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.finished(GeneralLoadUtils.java:865)
at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:31)
at javax.swing.SwingWorker$5.run(SwingWorker.java:717)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:814)
at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:95)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:824)
at javax.swing.Timer.fireActionPerformed(Timer.java:291)
at javax.swing.Timer$DoPostEvent.run(Timer.java:221)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677)
at java.awt.EventQueue.access$000(EventQueue.java:85)
at java.awt.EventQueue$1.run(EventQueue.java:638)
at java.awt.EventQueue$1.run(EventQueue.java:636)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:647)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Caused by: java.lang.OutOfMemoryError: Java heap space
at net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:374)
at net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:361)
at net.sf.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:109)
at net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:234)
at java.io.DataInputStream.read(DataInputStream.java:132)
at net.sf.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:394)
at net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:371)
at net.sf.samtools.util.BinaryCodec.readByteBuffer(BinaryCodec.java:480)
at net.sf.samtools.util.BinaryCodec.readInt(BinaryCodec.java:491)
at net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:159)
at net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:486)
at net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:594)
at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:460)
at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:450)
at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:417)
at net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.advance(BAMFileReader.java:674)
at net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:647)
at net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:602)
at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:629)
at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:607)
at com.affymetrix.genometryImpl.symloader.BAM.parse(BAM.java:135)
at com.affymetrix.genometryImpl.symloader.XAM.getRegion(XAM.java:122)
at com.affymetrix.igb.featureloader.QuickLoad.getRegion(QuickLoad.java:405)
at com.affymetrix.igb.featureloader.QuickLoad.loadAndAddSymmetries(QuickLoad.java:248)
at com.affymetrix.igb.featureloader.QuickLoad.loadSymmetriesThread(QuickLoad.java:177)
at com.affymetrix.igb.featureloader.QuickLoad.loadFeatures(QuickLoad.java:155)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:906)
at com.affymetrix.igb.view.load.GeneralLoadUtils.access$200(GeneralLoadUtils.java:88)
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:839)
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:834)
at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:38)
at javax.swing.SwingWorker$1.call(SwingWorker.java:277)
Attachments
Issue Links
- relates to
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BUG-623 File management bugs
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- Closed
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