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.
Fixed in r8431.