[BUG-331] NPE possibly when downloading sequence - JIRA UNCC

Details

Type: Bug
Status: Closed (View Workflow)
Priority: Major
Resolution: Fixed
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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

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BUG-622 File format issues

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Fuquan Wang (Inactive) added a comment - 05/Jun/12 12:53 PM

Passed on 7.0.0 (11818) Mac.

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Fuquan Wang (Inactive) added a comment - 05/Jun/12 12:53 PM Passed on 7.0.0 (11818) Mac.

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Alyssa Gulledge (Inactive) added a comment - 05/Mar/12 10:03 AM

passed mac

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Alyssa Gulledge (Inactive) added a comment - 05/Mar/12 10:03 AM passed mac

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Katharine Kubiak (Inactive) added a comment - 01/Mar/12 9:24 AM

Passed Windows v10527

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Katharine Kubiak (Inactive) added a comment - 01/Mar/12 9:24 AM Passed Windows v10527

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Alyssa Gulledge (Inactive) added a comment - 19/Jan/12 7:54 AM - 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.

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Alyssa Gulledge (Inactive) added a comment - 19/Jan/12 7:54 AM - 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.

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Katharine Kubiak (Inactive) added a comment - 18/Jan/12 7:56 AM

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)

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Katharine Kubiak (Inactive) added a comment - 18/Jan/12 7:56 AM 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)

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Hiral Vora (Inactive) added a comment - 12/Jul/11 5:49 AM

Fixed in r8431.

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Hiral Vora (Inactive) added a comment - 12/Jul/11 5:49 AM Fixed in r8431.

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Assignee:

Unassigned

Reporter:

Michael Lawrence (Inactive)

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Dates

Created:

24/Apr/11 5:46 PM

Updated:

18/Dec/12 6:41 AM

Resolved:

18/Dec/12 6:41 AM