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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)

              Attachments

                Issue Links

                relates to

                Task - A task that needs to be done. BUG-623 File management bugs

                • Blocker - Blocks development and/or testing work, production could not run.
                • Closed

                  Activity

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                  fwang4 Fuquan Wang (Inactive) added a comment -

                  Passed on 7.0.0 (11920) Mac.

                  Show
                  fwang4 Fuquan Wang (Inactive) added a comment - Passed on 7.0.0 (11920) Mac.
                  Hide
                  Permalink
                  anuj Anuj Puram (Inactive) added a comment -

                  I think its the problem with the size of the file this bug does not appear when we load in the files and zoom into the genomes of the wig files and bam files etc., the saving and loading of sessions occur without any problem.

                  The steps I performed to test this issue is as follows:

                  1) Load IGB
                  2) Loaded Arabidopsis__thailana genome and zoomed into it.
                  3) I dragged in the Bam file, Wig file and a bed file from browser onto IGB
                  4) Then I hit the load data button which made the files to be loaded onto IGB
                  5) Then I saved the session onto an xml file which was successfull
                  6) Then I restored IGB to default
                  7) reloaded IGB
                  8) Then loaded the session that has been saved which loaded successfully.

                  So, this was not an issue with load session option but rather it was due to the size of the bam file

                  Show
                  anuj Anuj Puram (Inactive) added a comment - I think its the problem with the size of the file this bug does not appear when we load in the files and zoom into the genomes of the wig files and bam files etc., the saving and loading of sessions occur without any problem. The steps I performed to test this issue is as follows: 1) Load IGB 2) Loaded Arabidopsis__thailana genome and zoomed into it. 3) I dragged in the Bam file, Wig file and a bed file from browser onto IGB 4) Then I hit the load data button which made the files to be loaded onto IGB 5) Then I saved the session onto an xml file which was successfull 6) Then I restored IGB to default 7) reloaded IGB 8) Then loaded the session that has been saved which loaded successfully. So, this was not an issue with load session option but rather it was due to the size of the bam file

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

                      • Created:
                        Updated:
                        Resolved: