INFO [2017-03-08 08:22:08,887] [Main.java:134]  Startup  IGV Version 2.3.90 (143)01/08/2017 11:43 PM
INFO [2017-03-08 08:22:08,903] [Main.java:135]  Java 1.8.0_101
INFO [2017-03-08 08:22:08,903] [Main.java:136]  Default User Directory: C:\Users\Mara\Documents
INFO [2017-03-08 08:22:08,903] [Main.java:137]  OS: Windows 7
INFO [2017-03-08 08:22:48,971] [GenomeManager.java:145]  Loading genome: C:\Users\Mara\Desktop\Triticum_aestivum.IWGSC1+popseq.31.cds.all.fa
INFO [2017-03-08 08:22:49,954] [GenomeManager.java:192]  Genome loaded.  id= C:\Users\Mara\Desktop\Triticum_aestivum.IWGSC1+popseq.31.cds.all.fa
INFO [2017-03-08 08:22:50,973] [CommandListener.java:106]  Listening on port 60151
INFO [2017-03-08 18:21:37,467] [ShutdownThread.java:51]  Shutting down
INFO [2017-03-10 10:18:33,418] [Main.java:134]  Startup  IGV Version 2.3.90 (143)01/08/2017 11:43 PM
INFO [2017-03-10 10:18:33,434] [Main.java:135]  Java 1.8.0_101
INFO [2017-03-10 10:18:33,434] [Main.java:136]  Default User Directory: C:\Users\Mara\Documents
INFO [2017-03-10 10:18:33,434] [Main.java:137]  OS: Windows 7
INFO [2017-03-10 10:18:52,216] [GenomeManager.java:145]  Loading genome: C:\Users\Mara\Desktop\Triticum_aestivum.IWGSC1+popseq.31.cds.all.fa
INFO [2017-03-10 10:18:52,996] [GenomeManager.java:192]  Genome loaded.  id= C:\Users\Mara\Desktop\Triticum_aestivum.IWGSC1+popseq.31.cds.all.fa
INFO [2017-03-10 10:18:54,197] [CommandListener.java:106]  Listening on port 60151
INFO [2017-03-10 10:24:28,723] [GenomeManager.java:145]  Loading genome: C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.zip
INFO [2017-03-10 10:24:28,765] [FastaUtils.java:66]  Creating index file at C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.zip.fai
ERROR [2017-03-10 10:24:28,863] [MessageUtils.java:64]  Could not create index file: C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.zip.fai
org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.zip<br>Blank line at line number 187, followed by data line at 188, in contig null
Blank lines are only allowed at the end of a contig
	at org.broad.igv.feature.genome.FastaUtils.createIndexFile(FastaUtils.java:144)
	at org.broad.igv.feature.genome.GenomeManager.loadFastaFile(GenomeManager.java:290)
	at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:167)
	at org.broad.igv.ui.IGV.loadGenome(IGV.java:690)
	at org.broad.igv.ui.IGV.loadGenome(IGV.java:671)
	at org.broad.igv.ui.IGV.doLoadGenome(IGV.java:633)
	at org.broad.igv.ui.IGVMenuBar$11.actionPerformed(IGVMenuBar.java:550)
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
	at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
	at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
	at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
	at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)
	at java.awt.Component.processMouseEvent(Component.java:6533)
	at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
	at java.awt.Component.processEvent(Component.java:6298)
	at java.awt.Container.processEvent(Container.java:2236)
	at java.awt.Component.dispatchEventImpl(Component.java:4889)
	at java.awt.Container.dispatchEventImpl(Container.java:2294)
	at java.awt.Component.dispatchEvent(Component.java:4711)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
	at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
	at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
	at java.awt.Container.dispatchEventImpl(Container.java:2280)
	at java.awt.Window.dispatchEventImpl(Window.java:2746)
	at java.awt.Component.dispatchEvent(Component.java:4711)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:731)
	at java.awt.EventQueue$4.run(EventQueue.java:729)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
ERROR [2017-03-10 10:24:28,930] [MessageUtils.java:74]  Could not create index file: C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.zip.fai
INFO [2017-03-10 10:24:37,186] [GenomeManager.java:192]  Genome loaded.  id= C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.zip
INFO [2017-03-10 10:24:56,700] [ShutdownThread.java:51]  Shutting down
INFO [2017-03-10 10:26:05,501] [Main.java:134]  Startup  IGV Version 2.3.90 (143)01/08/2017 11:43 PM
INFO [2017-03-10 10:26:05,501] [Main.java:135]  Java 1.8.0_101
INFO [2017-03-10 10:26:05,501] [Main.java:136]  Default User Directory: C:\Users\Mara\Documents
INFO [2017-03-10 10:26:05,501] [Main.java:137]  OS: Windows 7
INFO [2017-03-10 10:26:21,055] [GenomeManager.java:145]  Loading genome: C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.zip
INFO [2017-03-10 10:26:21,086] [GenomeManager.java:192]  Genome loaded.  id= C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.zip
INFO [2017-03-10 10:26:21,351] [CommandListener.java:106]  Listening on port 60151
ERROR [2017-03-10 10:27:13,876] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.NullPointerException
	at org.broad.igv.feature.genome.GenomeListItem.checkHasDownloadedSequence(GenomeListItem.java:141)
	at org.broad.igv.feature.genome.GenomeListItem.hasDownloadedSequence(GenomeListItem.java:122)
	at org.broad.igv.ui.ManageGenomesDialog$GenomeCellRenderer.getListCellRendererComponent(ManageGenomesDialog.java:419)
	at javax.swing.plaf.basic.BasicListUI.updateLayoutState(BasicListUI.java:1361)
	at javax.swing.plaf.basic.BasicListUI.maybeUpdateLayoutState(BasicListUI.java:1311)
	at javax.swing.plaf.basic.BasicListUI.getPreferredSize(BasicListUI.java:578)
	at javax.swing.JComponent.getPreferredSize(JComponent.java:1662)
	at javax.swing.JList.getPreferredScrollableViewportSize(JList.java:2447)
	at javax.swing.ViewportLayout.preferredLayoutSize(ViewportLayout.java:93)
	at java.awt.Container.preferredSize(Container.java:1796)
	at java.awt.Container.getPreferredSize(Container.java:1780)
	at javax.swing.JComponent.getPreferredSize(JComponent.java:1664)
	at javax.swing.ScrollPaneLayout.preferredLayoutSize(ScrollPaneLayout.java:492)
	at java.awt.Container.preferredSize(Container.java:1796)
	at java.awt.Container.getPreferredSize(Container.java:1780)
	at javax.swing.JComponent.getPreferredSize(JComponent.java:1664)
	at javax.swing.BoxLayout.checkRequests(BoxLayout.java:484)
	at javax.swing.BoxLayout.layoutContainer(BoxLayout.java:425)
	at java.awt.Container.layout(Container.java:1510)
	at java.awt.Container.doLayout(Container.java:1499)
	at java.awt.Container.validateTree(Container.java:1695)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validate(Container.java:1630)
	at java.awt.Container.validateUnconditionally(Container.java:1667)
	at java.awt.Dialog.conditionalShow(Dialog.java:908)
	at java.awt.Dialog.show(Dialog.java:1045)
	at java.awt.Component.show(Component.java:1671)
	at java.awt.Component.setVisible(Component.java:1623)
	at java.awt.Window.setVisible(Window.java:1014)
	at java.awt.Dialog.setVisible(Dialog.java:1005)
	at org.broad.igv.ui.IGVMenuBar$14.actionPerformed(IGVMenuBar.java:598)
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
	at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
	at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
	at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
	at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)
	at java.awt.Component.processMouseEvent(Component.java:6533)
	at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
	at java.awt.Component.processEvent(Component.java:6298)
	at java.awt.Container.processEvent(Container.java:2236)
	at java.awt.Component.dispatchEventImpl(Component.java:4889)
	at java.awt.Container.dispatchEventImpl(Container.java:2294)
	at java.awt.Component.dispatchEvent(Component.java:4711)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
	at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
	at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
	at java.awt.Container.dispatchEventImpl(Container.java:2280)
	at java.awt.Window.dispatchEventImpl(Window.java:2746)
	at java.awt.Component.dispatchEvent(Component.java:4711)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:731)
	at java.awt.EventQueue$4.run(EventQueue.java:729)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
ERROR [2017-03-10 10:27:13,939] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.NullPointerException
	at javax.swing.SizeRequirements.calculateAlignedPositions(SizeRequirements.java:461)
	at javax.swing.BoxLayout.layoutContainer(BoxLayout.java:435)
	at java.awt.Container.layout(Container.java:1510)
	at java.awt.Container.doLayout(Container.java:1499)
	at java.awt.Container.validateTree(Container.java:1695)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validate(Container.java:1630)
	at java.awt.Window.dispatchEventImpl(Window.java:2744)
	at java.awt.Component.dispatchEvent(Component.java:4711)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:731)
	at java.awt.EventQueue$4.run(EventQueue.java:729)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
ERROR [2017-03-10 10:27:13,939] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.NullPointerException
	at javax.swing.SizeRequirements.calculateAlignedPositions(SizeRequirements.java:461)
	at javax.swing.BoxLayout.layoutContainer(BoxLayout.java:435)
	at java.awt.Container.layout(Container.java:1510)
	at java.awt.Container.doLayout(Container.java:1499)
	at java.awt.Container.validateTree(Container.java:1695)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validate(Container.java:1630)
	at java.awt.Window.dispatchEventImpl(Window.java:2744)
	at java.awt.Component.dispatchEvent(Component.java:4711)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:731)
	at java.awt.EventQueue$4.run(EventQueue.java:729)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
ERROR [2017-03-10 10:27:13,939] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.NullPointerException
	at javax.swing.SizeRequirements.calculateAlignedPositions(SizeRequirements.java:461)
	at javax.swing.BoxLayout.layoutContainer(BoxLayout.java:435)
	at java.awt.Container.layout(Container.java:1510)
	at java.awt.Container.doLayout(Container.java:1499)
	at java.awt.Container.validateTree(Container.java:1695)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validate(Container.java:1630)
	at java.awt.Window.dispatchEventImpl(Window.java:2744)
	at java.awt.Component.dispatchEvent(Component.java:4711)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:731)
	at java.awt.EventQueue$4.run(EventQueue.java:729)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
INFO [2017-03-10 10:27:24,781] [ShutdownThread.java:51]  Shutting down
INFO [2017-03-10 10:27:32,334] [Main.java:134]  Startup  IGV Version 2.3.90 (143)01/08/2017 11:43 PM
INFO [2017-03-10 10:27:32,334] [Main.java:135]  Java 1.8.0_101
INFO [2017-03-10 10:27:32,334] [Main.java:136]  Default User Directory: C:\Users\Mara\Documents
INFO [2017-03-10 10:27:32,334] [Main.java:137]  OS: Windows 7
INFO [2017-03-10 10:27:49,213] [GenomeManager.java:145]  Loading genome: C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.zip
INFO [2017-03-10 10:27:49,307] [GenomeManager.java:192]  Genome loaded.  id= C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.zip
INFO [2017-03-10 10:27:49,603] [CommandListener.java:106]  Listening on port 60151
ERROR [2017-03-10 10:28:00,570] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.NullPointerException
	at org.broad.igv.feature.genome.GenomeListItem.checkHasDownloadedSequence(GenomeListItem.java:141)
	at org.broad.igv.feature.genome.GenomeListItem.hasDownloadedSequence(GenomeListItem.java:122)
	at org.broad.igv.ui.ManageGenomesDialog$GenomeCellRenderer.getListCellRendererComponent(ManageGenomesDialog.java:419)
	at javax.swing.plaf.basic.BasicListUI.updateLayoutState(BasicListUI.java:1361)
	at javax.swing.plaf.basic.BasicListUI.maybeUpdateLayoutState(BasicListUI.java:1311)
	at javax.swing.plaf.basic.BasicListUI.getPreferredSize(BasicListUI.java:578)
	at javax.swing.JComponent.getPreferredSize(JComponent.java:1662)
	at javax.swing.JList.getPreferredScrollableViewportSize(JList.java:2447)
	at javax.swing.ViewportLayout.preferredLayoutSize(ViewportLayout.java:93)
	at java.awt.Container.preferredSize(Container.java:1796)
	at java.awt.Container.getPreferredSize(Container.java:1780)
	at javax.swing.JComponent.getPreferredSize(JComponent.java:1664)
	at javax.swing.ScrollPaneLayout.preferredLayoutSize(ScrollPaneLayout.java:492)
	at java.awt.Container.preferredSize(Container.java:1796)
	at java.awt.Container.getPreferredSize(Container.java:1780)
	at javax.swing.JComponent.getPreferredSize(JComponent.java:1664)
	at javax.swing.BoxLayout.checkRequests(BoxLayout.java:484)
	at javax.swing.BoxLayout.layoutContainer(BoxLayout.java:425)
	at java.awt.Container.layout(Container.java:1510)
	at java.awt.Container.doLayout(Container.java:1499)
	at java.awt.Container.validateTree(Container.java:1695)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validate(Container.java:1630)
	at java.awt.Container.validateUnconditionally(Container.java:1667)
	at java.awt.Dialog.conditionalShow(Dialog.java:908)
	at java.awt.Dialog.show(Dialog.java:1045)
	at java.awt.Component.show(Component.java:1671)
	at java.awt.Component.setVisible(Component.java:1623)
	at java.awt.Window.setVisible(Window.java:1014)
	at java.awt.Dialog.setVisible(Dialog.java:1005)
	at org.broad.igv.ui.IGVMenuBar$14.actionPerformed(IGVMenuBar.java:598)
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
	at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
	at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
	at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
	at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)
	at java.awt.Component.processMouseEvent(Component.java:6533)
	at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
	at java.awt.Component.processEvent(Component.java:6298)
	at java.awt.Container.processEvent(Container.java:2236)
	at java.awt.Component.dispatchEventImpl(Component.java:4889)
	at java.awt.Container.dispatchEventImpl(Container.java:2294)
	at java.awt.Component.dispatchEvent(Component.java:4711)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
	at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
	at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
	at java.awt.Container.dispatchEventImpl(Container.java:2280)
	at java.awt.Window.dispatchEventImpl(Window.java:2746)
	at java.awt.Component.dispatchEvent(Component.java:4711)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:731)
	at java.awt.EventQueue$4.run(EventQueue.java:729)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
ERROR [2017-03-10 10:28:00,586] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.NullPointerException
	at javax.swing.SizeRequirements.calculateAlignedPositions(SizeRequirements.java:461)
	at javax.swing.BoxLayout.layoutContainer(BoxLayout.java:435)
	at java.awt.Container.layout(Container.java:1510)
	at java.awt.Container.doLayout(Container.java:1499)
	at java.awt.Container.validateTree(Container.java:1695)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validate(Container.java:1630)
	at java.awt.Window.dispatchEventImpl(Window.java:2744)
	at java.awt.Component.dispatchEvent(Component.java:4711)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:731)
	at java.awt.EventQueue$4.run(EventQueue.java:729)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
ERROR [2017-03-10 10:28:00,586] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.NullPointerException
	at javax.swing.SizeRequirements.calculateAlignedPositions(SizeRequirements.java:461)
	at javax.swing.BoxLayout.layoutContainer(BoxLayout.java:435)
	at java.awt.Container.layout(Container.java:1510)
	at java.awt.Container.doLayout(Container.java:1499)
	at java.awt.Container.validateTree(Container.java:1695)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validate(Container.java:1630)
	at java.awt.Window.dispatchEventImpl(Window.java:2744)
	at java.awt.Component.dispatchEvent(Component.java:4711)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:731)
	at java.awt.EventQueue$4.run(EventQueue.java:729)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
ERROR [2017-03-10 10:28:00,586] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.NullPointerException
	at javax.swing.SizeRequirements.calculateAlignedPositions(SizeRequirements.java:461)
	at javax.swing.BoxLayout.layoutContainer(BoxLayout.java:435)
	at java.awt.Container.layout(Container.java:1510)
	at java.awt.Container.doLayout(Container.java:1499)
	at java.awt.Container.validateTree(Container.java:1695)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validate(Container.java:1630)
	at java.awt.Window.dispatchEventImpl(Window.java:2744)
	at java.awt.Component.dispatchEvent(Component.java:4711)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:731)
	at java.awt.EventQueue$4.run(EventQueue.java:729)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
ERROR [2017-03-10 10:28:08,635] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.NullPointerException
	at org.broad.igv.feature.genome.GenomeListItem.checkHasDownloadedSequence(GenomeListItem.java:141)
	at org.broad.igv.feature.genome.GenomeListItem.hasDownloadedSequence(GenomeListItem.java:122)
	at org.broad.igv.ui.ManageGenomesDialog$GenomeCellRenderer.getListCellRendererComponent(ManageGenomesDialog.java:419)
	at javax.swing.plaf.basic.BasicListUI.updateLayoutState(BasicListUI.java:1361)
	at javax.swing.plaf.basic.BasicListUI.maybeUpdateLayoutState(BasicListUI.java:1311)
	at javax.swing.plaf.basic.BasicListUI.getPreferredSize(BasicListUI.java:578)
	at javax.swing.JComponent.getPreferredSize(JComponent.java:1662)
	at javax.swing.JList.getPreferredScrollableViewportSize(JList.java:2447)
	at javax.swing.ViewportLayout.preferredLayoutSize(ViewportLayout.java:93)
	at java.awt.Container.preferredSize(Container.java:1796)
	at java.awt.Container.getPreferredSize(Container.java:1780)
	at javax.swing.JComponent.getPreferredSize(JComponent.java:1664)
	at javax.swing.ScrollPaneLayout.preferredLayoutSize(ScrollPaneLayout.java:492)
	at java.awt.Container.preferredSize(Container.java:1796)
	at java.awt.Container.getPreferredSize(Container.java:1780)
	at javax.swing.JComponent.getPreferredSize(JComponent.java:1664)
	at javax.swing.BoxLayout.checkRequests(BoxLayout.java:484)
	at javax.swing.BoxLayout.layoutContainer(BoxLayout.java:425)
	at java.awt.Container.layout(Container.java:1510)
	at java.awt.Container.doLayout(Container.java:1499)
	at java.awt.Container.validateTree(Container.java:1695)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validate(Container.java:1630)
	at java.awt.Container.validateUnconditionally(Container.java:1667)
	at java.awt.Dialog.conditionalShow(Dialog.java:908)
	at java.awt.Dialog.show(Dialog.java:1045)
	at java.awt.Component.show(Component.java:1671)
	at java.awt.Component.setVisible(Component.java:1623)
	at java.awt.Window.setVisible(Window.java:1014)
	at java.awt.Dialog.setVisible(Dialog.java:1005)
	at org.broad.igv.ui.IGVMenuBar$14.actionPerformed(IGVMenuBar.java:598)
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
	at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
	at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
	at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
	at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)
	at java.awt.Component.processMouseEvent(Component.java:6533)
	at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
	at java.awt.Component.processEvent(Component.java:6298)
	at java.awt.Container.processEvent(Container.java:2236)
	at java.awt.Component.dispatchEventImpl(Component.java:4889)
	at java.awt.Container.dispatchEventImpl(Container.java:2294)
	at java.awt.Component.dispatchEvent(Component.java:4711)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
	at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
	at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
	at java.awt.Container.dispatchEventImpl(Container.java:2280)
	at java.awt.Window.dispatchEventImpl(Window.java:2746)
	at java.awt.Component.dispatchEvent(Component.java:4711)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:731)
	at java.awt.EventQueue$4.run(EventQueue.java:729)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
ERROR [2017-03-10 10:28:08,635] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.NullPointerException
	at javax.swing.SizeRequirements.calculateAlignedPositions(SizeRequirements.java:461)
	at javax.swing.BoxLayout.layoutContainer(BoxLayout.java:435)
	at java.awt.Container.layout(Container.java:1510)
	at java.awt.Container.doLayout(Container.java:1499)
	at java.awt.Container.validateTree(Container.java:1695)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validate(Container.java:1630)
	at java.awt.Window.dispatchEventImpl(Window.java:2744)
	at java.awt.Component.dispatchEvent(Component.java:4711)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:731)
	at java.awt.EventQueue$4.run(EventQueue.java:729)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
ERROR [2017-03-10 10:28:08,635] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.NullPointerException
	at javax.swing.SizeRequirements.calculateAlignedPositions(SizeRequirements.java:461)
	at javax.swing.BoxLayout.layoutContainer(BoxLayout.java:435)
	at java.awt.Container.layout(Container.java:1510)
	at java.awt.Container.doLayout(Container.java:1499)
	at java.awt.Container.validateTree(Container.java:1695)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validate(Container.java:1630)
	at java.awt.Window.dispatchEventImpl(Window.java:2744)
	at java.awt.Component.dispatchEvent(Component.java:4711)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:731)
	at java.awt.EventQueue$4.run(EventQueue.java:729)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
ERROR [2017-03-10 10:28:08,635] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.NullPointerException
	at javax.swing.SizeRequirements.calculateAlignedPositions(SizeRequirements.java:461)
	at javax.swing.BoxLayout.layoutContainer(BoxLayout.java:435)
	at java.awt.Container.layout(Container.java:1510)
	at java.awt.Container.doLayout(Container.java:1499)
	at java.awt.Container.validateTree(Container.java:1695)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validateTree(Container.java:1704)
	at java.awt.Container.validate(Container.java:1630)
	at java.awt.Window.dispatchEventImpl(Window.java:2744)
	at java.awt.Component.dispatchEvent(Component.java:4711)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:731)
	at java.awt.EventQueue$4.run(EventQueue.java:729)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
INFO [2017-03-10 10:28:18,167] [GenomeManager.java:145]  Loading genome: C:\Users\Mara\Desktop\Triticum_aestivum.IWGSC1+popseq.31.cds.all.fa
INFO [2017-03-10 10:28:18,884] [GenomeManager.java:192]  Genome loaded.  id= C:\Users\Mara\Desktop\Triticum_aestivum.IWGSC1+popseq.31.cds.all.fa
INFO [2017-03-10 10:28:32,987] [GenomeManager.java:145]  Loading genome: C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.fsa
INFO [2017-03-10 10:28:32,987] [FastaUtils.java:66]  Creating index file at C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.fsa.fai
INFO [2017-03-10 10:28:42,768] [GenomeManager.java:192]  Genome loaded.  id= C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.fsa
INFO [2017-03-10 10:29:46,417] [IGV.java:1704]  Loading 1 resources.
INFO [2017-03-10 10:29:46,417] [TrackLoader.java:126]  Loading resource, path C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.bam
INFO [2017-03-10 10:29:46,511] [BAMFileReader.java:162]  Index file: C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.bam.bai not found
INFO [2017-03-10 10:29:46,511] [BAMFileReader.java:163]  Index file: C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.bai not Found
INFO [2017-03-10 10:29:46,604] [MessageUtils.java:74]  Error loading SAM header: Sequence lengths > 2^29-1 are not supported
INFO [2017-03-10 10:29:54,841] [MessageUtils.java:74]  <html>Could not load index file for: C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.bam<br>  An index file is required for SAM & BAM files.
INFO [2017-03-10 10:37:06,394] [IGV.java:1704]  Loading 1 resources.
INFO [2017-03-10 10:37:06,394] [TrackLoader.java:126]  Loading resource, path C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bam.bai
INFO [2017-03-10 10:37:06,394] [MessageUtils.java:74]  <html><b>ERROR:</b> Loading SAM/BAM index files are not supported:  C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bam.bai<br>Load the SAM or BAM file directly. 
INFO [2017-03-10 10:38:22,272] [IGV.java:1704]  Loading 1 resources.
INFO [2017-03-10 10:38:22,272] [TrackLoader.java:126]  Loading resource, path C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bam
INFO [2017-03-10 10:38:22,303] [MessageUtils.java:74]  Error loading SAM header: Sequence lengths > 2^29-1 are not supported
INFO [2017-03-10 10:42:17,241] [IGV.java:1704]  Loading 1 resources.
INFO [2017-03-10 10:42:17,257] [TrackLoader.java:126]  Loading resource, path C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bam.bai
INFO [2017-03-10 10:42:17,257] [MessageUtils.java:74]  <html><b>ERROR:</b> Loading SAM/BAM index files are not supported:  C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bam.bai<br>Load the SAM or BAM file directly. 
INFO [2017-03-10 10:50:07,173] [ShutdownThread.java:51]  Shutting down
INFO [2017-03-10 10:50:27,861] [Main.java:134]  Startup  IGV Version 2.3.90 (143)01/08/2017 11:43 PM
INFO [2017-03-10 10:50:27,861] [Main.java:135]  Java 1.8.0_101
INFO [2017-03-10 10:50:27,861] [Main.java:136]  Default User Directory: C:\Users\Mara\Documents
INFO [2017-03-10 10:50:27,861] [Main.java:137]  OS: Windows 7
INFO [2017-03-10 10:50:43,524] [GenomeManager.java:145]  Loading genome: C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.fsa
INFO [2017-03-10 10:50:43,555] [GenomeManager.java:192]  Genome loaded.  id= C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.fsa
INFO [2017-03-10 10:50:43,820] [CommandListener.java:106]  Listening on port 60151
INFO [2017-03-10 10:51:42,741] [IGV.java:1704]  Loading 1 resources.
INFO [2017-03-10 10:51:42,741] [TrackLoader.java:126]  Loading resource, path C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bam
INFO [2017-03-10 10:51:42,851] [MessageUtils.java:74]  Error loading SAM header: Sequence lengths > 2^29-1 are not supported
INFO [2017-03-10 10:52:08,123] [IGV.java:1704]  Loading 1 resources.
INFO [2017-03-10 10:52:08,123] [TrackLoader.java:126]  Loading resource, path C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bam.bai
INFO [2017-03-10 10:52:08,123] [MessageUtils.java:74]  <html><b>ERROR:</b> Loading SAM/BAM index files are not supported:  C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bam.bai<br>Load the SAM or BAM file directly. 
ERROR [2017-03-10 10:57:55,363] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.ArrayIndexOutOfBoundsException: 3
	at org.broad.igv.sam.DenseAlignmentCounts.getMaxCount(DenseAlignmentCounts.java:111)
	at org.broad.igv.sam.AlignmentInterval.getMaxCount(AlignmentInterval.java:127)
	at org.broad.igv.sam.CoverageTrack.getInViewRange(CoverageTrack.java:360)
	at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:311)
	at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:283)
	at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:144)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JViewport.paint(JViewport.java:728)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JLayeredPane.paint(JLayeredPane.java:586)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
	at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579)
	at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502)
	at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
	at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
	at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
	at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
	at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
ERROR [2017-03-10 10:57:55,425] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.ArrayIndexOutOfBoundsException: 3
	at org.broad.igv.sam.DenseAlignmentCounts.getMaxCount(DenseAlignmentCounts.java:111)
	at org.broad.igv.sam.AlignmentInterval.getMaxCount(AlignmentInterval.java:127)
	at org.broad.igv.sam.CoverageTrack.getInViewRange(CoverageTrack.java:360)
	at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:311)
	at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:283)
	at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:144)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JViewport.paint(JViewport.java:728)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JLayeredPane.paint(JLayeredPane.java:586)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
	at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579)
	at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502)
	at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
	at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
	at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
	at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
	at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
ERROR [2017-03-10 10:57:55,457] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.ArrayIndexOutOfBoundsException: 3
	at org.broad.igv.sam.DenseAlignmentCounts.getMaxCount(DenseAlignmentCounts.java:111)
	at org.broad.igv.sam.AlignmentInterval.getMaxCount(AlignmentInterval.java:127)
	at org.broad.igv.sam.CoverageTrack.getInViewRange(CoverageTrack.java:360)
	at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:311)
	at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:283)
	at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:144)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JViewport.paint(JViewport.java:728)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JLayeredPane.paint(JLayeredPane.java:586)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
	at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579)
	at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502)
	at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
	at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
	at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
	at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
	at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
ERROR [2017-03-10 10:57:55,550] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.ArrayIndexOutOfBoundsException: 2
	at org.broad.igv.sam.DenseAlignmentCounts.getMaxCount(DenseAlignmentCounts.java:111)
	at org.broad.igv.sam.AlignmentInterval.getMaxCount(AlignmentInterval.java:127)
	at org.broad.igv.sam.CoverageTrack.getInViewRange(CoverageTrack.java:360)
	at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:311)
	at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:283)
	at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:144)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JViewport.paint(JViewport.java:728)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JLayeredPane.paint(JLayeredPane.java:586)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
	at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579)
	at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502)
	at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
	at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
	at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
	at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
	at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
ERROR [2017-03-10 10:57:55,644] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.ArrayIndexOutOfBoundsException: 2
	at org.broad.igv.sam.DenseAlignmentCounts.getMaxCount(DenseAlignmentCounts.java:111)
	at org.broad.igv.sam.AlignmentInterval.getMaxCount(AlignmentInterval.java:127)
	at org.broad.igv.sam.CoverageTrack.getInViewRange(CoverageTrack.java:360)
	at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:311)
	at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:283)
	at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:144)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JViewport.paint(JViewport.java:728)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JLayeredPane.paint(JLayeredPane.java:586)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
	at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579)
	at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502)
	at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
	at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
	at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
	at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
	at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
ERROR [2017-03-10 10:57:55,737] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.ArrayIndexOutOfBoundsException: 2
	at org.broad.igv.sam.DenseAlignmentCounts.getMaxCount(DenseAlignmentCounts.java:111)
	at org.broad.igv.sam.AlignmentInterval.getMaxCount(AlignmentInterval.java:127)
	at org.broad.igv.sam.CoverageTrack.getInViewRange(CoverageTrack.java:360)
	at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:311)
	at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:283)
	at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:144)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JViewport.paint(JViewport.java:728)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JLayeredPane.paint(JLayeredPane.java:586)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
	at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579)
	at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502)
	at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
	at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
	at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
	at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
	at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
ERROR [2017-03-10 10:57:55,831] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.ArrayIndexOutOfBoundsException: 2
	at org.broad.igv.sam.DenseAlignmentCounts.getMaxCount(DenseAlignmentCounts.java:111)
	at org.broad.igv.sam.AlignmentInterval.getMaxCount(AlignmentInterval.java:127)
	at org.broad.igv.sam.CoverageTrack.getInViewRange(CoverageTrack.java:360)
	at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:311)
	at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:283)
	at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:144)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JViewport.paint(JViewport.java:728)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JLayeredPane.paint(JLayeredPane.java:586)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
	at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579)
	at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502)
	at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
	at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
	at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
	at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
	at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
ERROR [2017-03-10 10:57:55,925] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.ArrayIndexOutOfBoundsException: 2
	at org.broad.igv.sam.DenseAlignmentCounts.getMaxCount(DenseAlignmentCounts.java:111)
	at org.broad.igv.sam.AlignmentInterval.getMaxCount(AlignmentInterval.java:127)
	at org.broad.igv.sam.CoverageTrack.getInViewRange(CoverageTrack.java:360)
	at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:311)
	at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:283)
	at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:144)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JViewport.paint(JViewport.java:728)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JLayeredPane.paint(JLayeredPane.java:586)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
	at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579)
	at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502)
	at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
	at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
	at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
	at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
	at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
ERROR [2017-03-10 10:57:59,201] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.ArrayIndexOutOfBoundsException
ERROR [2017-03-10 10:57:59,279] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.ArrayIndexOutOfBoundsException
ERROR [2017-03-10 10:57:59,341] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.ArrayIndexOutOfBoundsException
INFO [2017-03-10 11:07:01,079] [ShutdownThread.java:51]  Shutting down
INFO [2017-03-10 11:07:05,560] [Main.java:134]  Startup  IGV Version 2.3.90 (143)01/08/2017 11:43 PM
INFO [2017-03-10 11:07:05,560] [Main.java:135]  Java 1.8.0_101
INFO [2017-03-10 11:07:05,560] [Main.java:136]  Default User Directory: C:\Users\Mara\Documents
INFO [2017-03-10 11:07:05,560] [Main.java:137]  OS: Windows 7
INFO [2017-03-10 11:07:17,665] [GenomeManager.java:145]  Loading genome: C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.fsa
INFO [2017-03-10 11:07:17,681] [GenomeManager.java:192]  Genome loaded.  id= C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.fsa
INFO [2017-03-10 11:07:17,837] [CommandListener.java:106]  Listening on port 60151
INFO [2017-03-10 11:08:16,742] [GenomeManager.java:145]  Loading genome: C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.fsa
INFO [2017-03-10 11:08:16,742] [GenomeManager.java:192]  Genome loaded.  id= C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.fsa
INFO [2017-03-10 11:08:55,009] [IGV.java:1704]  Loading 1 resources.
INFO [2017-03-10 11:08:55,009] [TrackLoader.java:126]  Loading resource, path C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.bam
INFO [2017-03-10 11:08:55,025] [BAMFileReader.java:162]  Index file: C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.bam.bai not found
INFO [2017-03-10 11:08:55,025] [BAMFileReader.java:163]  Index file: C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.bai not Found
INFO [2017-03-10 11:08:55,103] [MessageUtils.java:74]  Error loading SAM header: Sequence lengths > 2^29-1 are not supported
INFO [2017-03-10 11:16:41,725] [MessageUtils.java:74]  <html>Could not load index file for: C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.bam<br>  An index file is required for SAM & BAM files.
INFO [2017-03-10 11:16:50,414] [IGV.java:1704]  Loading 1 resources.
INFO [2017-03-10 11:16:50,414] [TrackLoader.java:126]  Loading resource, path C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bam.csi
INFO [2017-03-10 11:16:50,477] [MessageUtils.java:74]  <html>Unknown file type: C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bam.csi<br>Check file extension
INFO [2017-03-10 11:17:02,676] [ShutdownThread.java:51]  Shutting down
INFO [2017-03-10 11:17:06,595] [Main.java:134]  Startup  IGV Version 2.3.90 (143)01/08/2017 11:43 PM
INFO [2017-03-10 11:17:06,595] [Main.java:135]  Java 1.8.0_101
INFO [2017-03-10 11:17:06,595] [Main.java:136]  Default User Directory: C:\Users\Mara\Documents
INFO [2017-03-10 11:17:06,595] [Main.java:137]  OS: Windows 7
INFO [2017-03-10 11:17:18,607] [GenomeManager.java:145]  Loading genome: C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.fsa
INFO [2017-03-10 11:17:18,622] [GenomeManager.java:192]  Genome loaded.  id= C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.fsa
INFO [2017-03-10 11:17:18,763] [CommandListener.java:106]  Listening on port 60151
INFO [2017-03-10 11:17:43,208] [GenomeManager.java:145]  Loading genome: C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.fsa
INFO [2017-03-10 11:17:43,208] [GenomeManager.java:192]  Genome loaded.  id= C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.fsa
INFO [2017-03-10 11:18:21,053] [IGV.java:1704]  Loading 1 resources.
INFO [2017-03-10 11:18:21,053] [TrackLoader.java:126]  Loading resource, path C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bam
INFO [2017-03-10 11:18:21,100] [MessageUtils.java:74]  Error loading SAM header: Sequence lengths > 2^29-1 are not supported
INFO [2017-03-10 11:33:32,654] [IGV.java:1704]  Loading 1 resources.
INFO [2017-03-10 11:33:32,654] [TrackLoader.java:126]  Loading resource, path C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bam
INFO [2017-03-10 11:33:32,670] [MessageUtils.java:74]  Error loading SAM header: Sequence lengths > 2^29-1 are not supported
INFO [2017-03-10 11:37:23,696] [IGV.java:1704]  Loading 1 resources.
INFO [2017-03-10 11:37:23,696] [TrackLoader.java:126]  Loading resource, path C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bam
INFO [2017-03-10 11:37:23,696] [MessageUtils.java:74]  Error loading SAM header: Sequence lengths > 2^29-1 are not supported
INFO [2017-03-10 11:41:41,580] [ShutdownThread.java:51]  Shutting down
INFO [2017-03-10 11:41:46,543] [Main.java:134]  Startup  IGV Version 2.3.90 (143)01/08/2017 11:43 PM
INFO [2017-03-10 11:41:46,544] [Main.java:135]  Java 1.8.0_101
INFO [2017-03-10 11:41:46,544] [Main.java:136]  Default User Directory: C:\Users\Mara\Documents
INFO [2017-03-10 11:41:46,544] [Main.java:137]  OS: Windows 7
INFO [2017-03-10 11:41:59,293] [GenomeManager.java:145]  Loading genome: C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.fsa
INFO [2017-03-10 11:41:59,309] [GenomeManager.java:192]  Genome loaded.  id= C:\Users\Mara\Downloads\IWGSC refseq v1 genome\IWGSC_RefSeq_V1_chr2A.fsa
INFO [2017-03-10 11:41:59,460] [CommandListener.java:106]  Listening on port 60151
INFO [2017-03-10 11:42:15,077] [IGV.java:1704]  Loading 1 resources.
INFO [2017-03-10 11:42:15,081] [TrackLoader.java:126]  Loading resource, path C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bam
INFO [2017-03-10 11:42:15,104] [BAMFileReader.java:162]  Index file: C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bam.bai not found
INFO [2017-03-10 11:42:15,105] [BAMFileReader.java:163]  Index file: C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bai not Found
INFO [2017-03-10 11:42:15,132] [MessageUtils.java:74]  Error loading SAM header: Sequence lengths > 2^29-1 are not supported
INFO [2017-03-10 11:42:22,027] [MessageUtils.java:74]  <html>Could not load index file for: C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bam<br>  An index file is required for SAM & BAM files.
INFO [2017-03-10 11:42:54,698] [IGV.java:1704]  Loading 1 resources.
INFO [2017-03-10 11:42:54,699] [TrackLoader.java:126]  Loading resource, path C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.bam
INFO [2017-03-10 11:42:54,701] [BAMFileReader.java:162]  Index file: C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.bam.bai not found
INFO [2017-03-10 11:42:54,703] [BAMFileReader.java:163]  Index file: C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.bai not Found
INFO [2017-03-10 11:42:54,705] [MessageUtils.java:74]  Error loading SAM header: Sequence lengths > 2^29-1 are not supported
INFO [2017-03-10 11:42:55,876] [MessageUtils.java:74]  <html>Could not load index file for: C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.bam<br>  An index file is required for SAM & BAM files.
INFO [2017-03-10 11:58:25,143] [MessageUtils.java:74]  IGV is up to date
INFO [2017-03-10 12:14:38,418] [IGV.java:1704]  Loading 1 resources.
INFO [2017-03-10 12:14:38,418] [TrackLoader.java:126]  Loading resource, path C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bam
INFO [2017-03-10 12:14:38,419] [BAMFileReader.java:162]  Index file: C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bam.bai not found
INFO [2017-03-10 12:14:38,419] [BAMFileReader.java:163]  Index file: C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bai not Found
INFO [2017-03-10 12:14:38,421] [MessageUtils.java:74]  Error loading SAM header: Sequence lengths > 2^29-1 are not supported
INFO [2017-03-10 12:15:23,143] [MessageUtils.java:74]  <html>Could not load index file for: C:\Users\Mara\Documents\Colocalization analysis\SNP.alignment.sorted.bam<br>  An index file is required for SAM & BAM files.