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  1. Bug Repository
  2. BUG-331

NPE possibly when downloading sequence

    Details

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

      Description

      Hi guys,

      Robert handed me this:


      INFO: URL: http://netaffxdas.affymetrix.com/quickload_data/H_sapiens_Feb_2009/chr1.bnib Response Code: 200
      java.lang.NullPointerException
      at com.affymetrix.genometryImpl.symmetry.SimpleMutableSeqSymmetry.removeChild(SimpleMutableSeqSymmetry.java:56)
      at com.affymetrix.genometryImpl.BioSeq.removeAnnotation(BioSeq.java:332)
      at com.affymetrix.genometryImpl.BioSeq.removeAnnotation(BioSeq.java:310)
      at com.affymetrix.igb.view.DependentData.createTier(DependentData.java:63)
      at com.affymetrix.igb.view.TrackView.updateDependentData(TrackView.java:288)
      at com.affymetrix.igb.featureloader.QuickLoad$1.doInBackground(QuickLoad.java:177)
      at com.affymetrix.igb.featureloader.QuickLoad$1.doInBackground(QuickLoad.java:161)
      at javax.swing.SwingWorker$1.call(SwingWorker.java:274)
      at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
      at java.util.concurrent.FutureTask.run(FutureTask.java:138)
      at javax.swing.SwingWorker.run(SwingWorker.java:313)
      at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
      at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
      at java.lang.Thread.run(Thread.java:637)

      Not sure what triggers this - but there are quite a few in the console (and this seems to be the only exception, there
      are a few other tidbits of INFO),

      Obviously, this is not a lot to go on, but maybe it's enough of a hint?

      Thanks

        Attachments

          Issue Links

            Activity

            michafla Michael Lawrence (Inactive) created issue -
            hiralv Hiral Vora (Inactive) made changes -
            Field Original Value New Value
            Assignee Ann Loraine [ aloraine ] Hiral Vora [ hiralv ]
            Hide
            hiralv Hiral Vora (Inactive) added a comment -

            Fixed in r8431.

            Show
            hiralv Hiral Vora (Inactive) added a comment - Fixed in r8431.
            hiralv Hiral Vora (Inactive) made changes -
            Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Status Open [ 1 ] Resolved [ 5 ]
            Resolution Fixed [ 1 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Status Resolved [ 5 ] Closed [ 6 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Resolution Fixed [ 1 ]
            Status Closed [ 6 ] Reopened [ 4 ]
            david David Norris (Inactive) made changes -
            Assignee Alyssa Gulledge [ alyssa ]
            david David Norris (Inactive) made changes -
            Status Reopened [ 4 ] Resolved [ 5 ]
            Resolution Fixed [ 1 ]
            david David Norris (Inactive) made changes -
            Status Resolved [ 5 ] Closed [ 6 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Resolution Fixed [ 1 ]
            Status Closed [ 6 ] Reopened [ 4 ]
            Assignee Katharine Kubiak [ kkubiak ]
            Hide
            kkubiak Katharine Kubiak (Inactive) added a comment -

            I saved the file to desktop and dragged it into IGB.
            Console:

            INFO: Chromosome: chr1 : residues: 249,250,620
            Jan 18, 2012 12:55:03 PM com.affymetrix.igb.view.load.GeneralLoadUtils$2 finished
            SEVERE: Unable to get refresh action result.
            java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: Java heap space
            at java.util.concurrent.FutureTask$Sync.innerGet(Unknown Source)
            at java.util.concurrent.FutureTask.get(Unknown Source)
            at javax.swing.SwingWorker.get(Unknown Source)
            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$5.run(Unknown Source)
            at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(Unknown Source)
            at sun.swing.AccumulativeRunnable.run(Unknown Source)
            at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(Unknown Source)
            at javax.swing.Timer.fireActionPerformed(Unknown Source)
            at javax.swing.Timer$DoPostEvent.run(Unknown Source)
            at java.awt.event.InvocationEvent.dispatch(Unknown Source)
            at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
            at java.awt.EventQueue.access$000(Unknown Source)
            at java.awt.EventQueue$1.run(Unknown Source)
            at java.awt.EventQueue$1.run(Unknown Source)
            at java.security.AccessController.doPrivileged(Native Method)
            at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
            at java.awt.EventQueue.dispatchEvent(Unknown Source)
            at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
            at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
            at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
            at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
            at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
            at java.awt.EventDispatchThread.run(Unknown Source)
            Caused by: java.lang.OutOfMemoryError: Java heap space
            at java.lang.StringCoding$StringDecoder.decode(Unknown Source)
            at java.lang.StringCoding.decode(Unknown Source)
            at java.lang.StringCoding.decode(Unknown Source)
            at java.lang.String.<init>(Unknown Source)
            at java.lang.String.<init>(Unknown Source)
            at com.affymetrix.genometryImpl.symloader.BNIB.getRegionResidues(BNIB.java:89)
            at com.affymetrix.genometryImpl.symloader.ResidueTrackSymLoader.getRegionResidues(ResidueTrackSymLoader.java:61)
            at com.affymetrix.genometryImpl.symloader.ResidueTrackSymLoader.getResidueTrack(ResidueTrackSymLoader.java:66)
            at com.affymetrix.genometryImpl.symloader.ResidueTrackSymLoader.getRegion(ResidueTrackSymLoader.java:56)
            at com.affymetrix.igb.featureloader.QuickLoad.getRegion(QuickLoad.java:402)
            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$1.call(Unknown Source)
            at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
            at java.util.concurrent.FutureTask.run(Unknown Source)
            at javax.swing.SwingWorker.run(Unknown Source)
            at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
            at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
            at java.lang.Thread.run(Unknown Source)

            Show
            kkubiak Katharine Kubiak (Inactive) added a comment - I saved the file to desktop and dragged it into IGB. Console: INFO: Chromosome: chr1 : residues: 249,250,620 Jan 18, 2012 12:55:03 PM com.affymetrix.igb.view.load.GeneralLoadUtils$2 finished SEVERE: Unable to get refresh action result. java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: Java heap space at java.util.concurrent.FutureTask$Sync.innerGet(Unknown Source) at java.util.concurrent.FutureTask.get(Unknown Source) at javax.swing.SwingWorker.get(Unknown Source) 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$5.run(Unknown Source) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(Unknown Source) at sun.swing.AccumulativeRunnable.run(Unknown Source) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(Unknown Source) at javax.swing.Timer.fireActionPerformed(Unknown Source) at javax.swing.Timer$DoPostEvent.run(Unknown Source) at java.awt.event.InvocationEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$000(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) Caused by: java.lang.OutOfMemoryError: Java heap space at java.lang.StringCoding$StringDecoder.decode(Unknown Source) at java.lang.StringCoding.decode(Unknown Source) at java.lang.StringCoding.decode(Unknown Source) at java.lang.String.<init>(Unknown Source) at java.lang.String.<init>(Unknown Source) at com.affymetrix.genometryImpl.symloader.BNIB.getRegionResidues(BNIB.java:89) at com.affymetrix.genometryImpl.symloader.ResidueTrackSymLoader.getRegionResidues(ResidueTrackSymLoader.java:61) at com.affymetrix.genometryImpl.symloader.ResidueTrackSymLoader.getResidueTrack(ResidueTrackSymLoader.java:66) at com.affymetrix.genometryImpl.symloader.ResidueTrackSymLoader.getRegion(ResidueTrackSymLoader.java:56) at com.affymetrix.igb.featureloader.QuickLoad.getRegion(QuickLoad.java:402) 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$1.call(Unknown Source) at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source)
            kkubiak Katharine Kubiak (Inactive) made changes -
            Assignee Katharine Kubiak [ kkubiak ] Alyssa Gulledge [ alyssa ]
            Hide
            alyssa Alyssa Gulledge (Inactive) added a comment - - edited

            Katy uses the 1 GB version, I use the 2 GB version of IGB

            If I just drag it in and load (No species selected OR matching species/genome/chr#) OR if I 'Open file...' load I get a very similar error:

            Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: Java heap space
            at java.lang.String.toCharArray(String.java:2725)
            at com.affymetrix.igb.shared.AbstractAlignedTextGlyph.setResidueMask(AbstractAlignedTextGlyph.java:80)
            at com.affymetrix.igb.glyph.GenericAnnotGlyphFactory.handleAlignedResidues(GenericAnnotGlyphFactory.java:499)
            at com.affymetrix.igb.glyph.GenericAnnotGlyphFactory.determinePGlyph(GenericAnnotGlyphFactory.java:250)
            at com.affymetrix.igb.glyph.GenericAnnotGlyphFactory.addToTier(GenericAnnotGlyphFactory.java:228)
            at com.affymetrix.igb.glyph.GenericAnnotGlyphFactory.addLeafsToTier(GenericAnnotGlyphFactory.java:196)
            at com.affymetrix.igb.glyph.GenericAnnotGlyphFactory.addLeafsToTier(GenericAnnotGlyphFactory.java:193)
            at com.affymetrix.igb.glyph.GenericAnnotGlyphFactory.createDepthGlyph(GenericAnnotGlyphFactory.java:163)
            at com.affymetrix.igb.glyph.GenericAnnotGlyphFactory.createGlyph(GenericAnnotGlyphFactory.java:146)
            at com.affymetrix.igb.stylesheet.XmlStylesheetGlyphFactory.createGlyph(XmlStylesheetGlyphFactory.java:84)
            at com.affymetrix.igb.view.TrackView.addAnnotationGlyphs(TrackView.java:238)
            at com.affymetrix.igb.view.TrackView.addTracks(TrackView.java:201)
            at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1004)
            at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:845)
            at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:725)
            at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:652)
            at com.affymetrix.igb.view.load.GeneralLoadUtils$2.finished(GeneralLoadUtils.java:853)
            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)

            However, if this file is 'Open as Reference Sequence...' either no species OR proper homos sapies/genome version/chr1 there is no error on the 2 GB version (but it uses an incredible amount of memory).

            BUG: In the 1 GB version, loading as Ref Seq, what happens is that it tries to load, gives up and remains as 'No data loaded'. It throws no errors BUT you do NOT get the red warning icon in the Data Management table indicating a failure to load AND you get no warning that the file is too large to load.

            Show
            alyssa Alyssa Gulledge (Inactive) added a comment - - edited Katy uses the 1 GB version, I use the 2 GB version of IGB If I just drag it in and load (No species selected OR matching species/genome/chr#) OR if I 'Open file...' load I get a very similar error: Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: Java heap space at java.lang.String.toCharArray(String.java:2725) at com.affymetrix.igb.shared.AbstractAlignedTextGlyph.setResidueMask(AbstractAlignedTextGlyph.java:80) at com.affymetrix.igb.glyph.GenericAnnotGlyphFactory.handleAlignedResidues(GenericAnnotGlyphFactory.java:499) at com.affymetrix.igb.glyph.GenericAnnotGlyphFactory.determinePGlyph(GenericAnnotGlyphFactory.java:250) at com.affymetrix.igb.glyph.GenericAnnotGlyphFactory.addToTier(GenericAnnotGlyphFactory.java:228) at com.affymetrix.igb.glyph.GenericAnnotGlyphFactory.addLeafsToTier(GenericAnnotGlyphFactory.java:196) at com.affymetrix.igb.glyph.GenericAnnotGlyphFactory.addLeafsToTier(GenericAnnotGlyphFactory.java:193) at com.affymetrix.igb.glyph.GenericAnnotGlyphFactory.createDepthGlyph(GenericAnnotGlyphFactory.java:163) at com.affymetrix.igb.glyph.GenericAnnotGlyphFactory.createGlyph(GenericAnnotGlyphFactory.java:146) at com.affymetrix.igb.stylesheet.XmlStylesheetGlyphFactory.createGlyph(XmlStylesheetGlyphFactory.java:84) at com.affymetrix.igb.view.TrackView.addAnnotationGlyphs(TrackView.java:238) at com.affymetrix.igb.view.TrackView.addTracks(TrackView.java:201) at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1004) at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:845) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:725) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:652) at com.affymetrix.igb.view.load.GeneralLoadUtils$2.finished(GeneralLoadUtils.java:853) 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) However, if this file is 'Open as Reference Sequence...' either no species OR proper homos sapies/genome version/chr1 there is no error on the 2 GB version (but it uses an incredible amount of memory). BUG : In the 1 GB version, loading as Ref Seq, what happens is that it tries to load, gives up and remains as 'No data loaded'. It throws no errors BUT you do NOT get the red warning icon in the Data Management table indicating a failure to load AND you get no warning that the file is too large to load.
            alyssa Alyssa Gulledge (Inactive) made changes -
            Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
            hiralv Hiral Vora (Inactive) made changes -
            Project Bug Repository [ 10030 ] IGB 7.0 [ 10140 ]
            Key BUG-101 IGBC-61
            hiralv Hiral Vora (Inactive) made changes -
            Assignee Hiral Vora [ hiralv ]
            Hide
            kkubiak Katharine Kubiak (Inactive) added a comment -

            Passed Windows v10527

            Show
            kkubiak Katharine Kubiak (Inactive) added a comment - Passed Windows v10527
            kkubiak Katharine Kubiak (Inactive) made changes -
            Assignee Alyssa Gulledge [ alyssa ]
            Hide
            alyssa Alyssa Gulledge (Inactive) added a comment -

            passed mac

            Show
            alyssa Alyssa Gulledge (Inactive) added a comment - passed mac
            alyssa Alyssa Gulledge (Inactive) made changes -
            Status Reopened [ 4 ] Resolved [ 5 ]
            Assignee Alyssa Gulledge [ alyssa ]
            Resolution Fixed [ 1 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Status Resolved [ 5 ] Closed [ 6 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Project IGB 7.0 [ 10140 ] Bug Repository [ 10030 ]
            Key IGBC-61 BUG-331
            fwang4 Fuquan Wang (Inactive) made changes -
            Resolution Fixed [ 1 ]
            Status Closed [ 6 ] Reopened [ 4 ]
            Assignee Fuquan Wang [ fwang4 ]
            Hide
            fwang4 Fuquan Wang (Inactive) added a comment -

            Passed on 7.0.0 (11818) Mac.

            Show
            fwang4 Fuquan Wang (Inactive) added a comment - Passed on 7.0.0 (11818) Mac.
            fwang4 Fuquan Wang (Inactive) made changes -
            Status Reopened [ 4 ] Resolved [ 5 ]
            Assignee Fuquan Wang [ fwang4 ]
            Resolution Fixed [ 1 ]
            richard Richard Linchangco (Inactive) made changes -
            Resolution Fixed [ 1 ]
            Status Resolved [ 5 ] Reopened [ 4 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Link This issue relates to BUG-622 [ BUG-622 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Status Reopened [ 4 ] Closed [ 6 ]
            Resolution Fixed [ 1 ]

              People

              • Assignee:
                Unassigned
                Reporter:
                michafla Michael Lawrence (Inactive)
              • Votes:
                0 Vote for this issue
                Watchers:
                0 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: