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  1. Bug Repository
  2. BUG-266

An Exception in the Console when we try to load a complex session comprising of different kind of files

    Details

    • Type: Bug
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Fixed
    • Labels:
      None
    • 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)

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              • Assignee:
                Unassigned
                Reporter:
                anuj Anuj Puram (Inactive)
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                Dates

                • Created:
                  Updated:
                  Resolved: