{"action":"created","issue":{"url":"https://api.github.com/repos/igvteam/igv/issues/221","repository_url":"https://api.github.com/repos/igvteam/igv","labels_url":"https://api.github.com/repos/igvteam/igv/issues/221/labels{/name}","comments_url":"https://api.github.com/repos/igvteam/igv/issues/221/comments","events_url":"https://api.github.com/repos/igvteam/igv/issues/221/events","html_url":"https://github.com/igvteam/igv/issues/221","id":146488958,"number":221,"title":"Error in displaying application","user":{"login":"18209018","id":1442522,"avatar_url":"https://avatars.githubusercontent.com/u/1442522?v=3","gravatar_id":"","url":"https://api.github.com/users/18209018","html_url":"https://github.com/18209018","followers_url":"https://api.github.com/users/18209018/followers","following_url":"https://api.github.com/users/18209018/following{/other_user}","gists_url":"https://api.github.com/users/18209018/gists{/gist_id}","starred_url":"https://api.github.com/users/18209018/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/18209018/subscriptions","organizations_url":"https://api.github.com/users/18209018/orgs","repos_url":"https://api.github.com/users/18209018/repos","events_url":"https://api.github.com/users/18209018/events{/privacy}","received_events_url":"https://api.github.com/users/18209018/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2016-04-07T02:21:35Z","updated_at":"2016-04-07T14:45:41Z","closed_at":null,"body":"Hello, I use IGV 2.3.72 in Linux Ubuntu KDE Plasma. I got an error in displaying the application (basically, the GUI is messed up, the menu is not shown, the click action is not working,etc.) like below:\r\n\r\n`INFO [2016-04-07 11:13:17,690]  [DirectoryManager.java:163] [main]  IGV Directory: /home/bharata/igv\r\nINFO [2016-04-07 11:13:17,690] [DirectoryManager.java:163]  IGV Directory: /home/bharata/igv\r\nINFO [2016-04-07 11:13:17,694]  [Main.java:99] [main]  Startup  IGV Version 2.3.72 (105)04/01/2016 11:33 AM\r\nINFO [2016-04-07 11:13:17,694]  [Main.java:100] [main]  Java 1.8.0_45\r\nINFO [2016-04-07 11:13:17,694]  [DirectoryManager.java:72] [main]  Fetching user directory... \r\nINFO [2016-04-07 11:13:17,804]  [Main.java:101] [main]  Default User Directory: /home/bharata\r\nINFO [2016-04-07 11:13:17,804]  [Main.java:102] [main]  OS: Linux\r\nINFO [2016-04-07 11:13:30,088]  [GenomeManager.java:145] [main]  Loading genome: /home/local/EnsembleHG38-80/Ch38.cdna.all.fa.fai\r\nINFO [2016-04-07 11:13:30,635]  [GenomeManager.java:192] [main]  Genome loaded.  id= /home/local/EnsembleHG38-80/Ch38.cdna.all.fa\r\nINFO [2016-04-07 11:13:31,345]  [CommandListener.java:106] [Thread-6]  Listening on port 60151\r\nERROR [2016-04-07 11:13:31,699]  [DefaultExceptionHandler.java:49] [AWT-EventQueue-0]  Unhandled exception\r\njava.lang.NegativeArraySizeException\r\n        at org.broad.igv.ui.panel.ZoomSliderPanel.updateTickCount(ZoomSliderPanel.java:103)\r\n        at org.broad.igv.ui.panel.ZoomSliderPanel.paintComponent(ZoomSliderPanel.java:112)\r\n        at javax.swing.JComponent.paint(JComponent.java:1056)\r\n        at javax.swing.JComponent.paintChildren(JComponent.java:889)\r\n        at javax.swing.JComponent.paint(JComponent.java:1065)\r\n        at javax.swing.JComponent.paintChildren(JComponent.java:889)\r\n        at javax.swing.JComponent.paint(JComponent.java:1065)\r\n        at javax.swing.JComponent.paintChildren(JComponent.java:889)\r\n        at javax.swing.JComponent.paint(JComponent.java:1065)\r\n        at javax.swing.JComponent.paintChildren(JComponent.java:889)\r\n        at javax.swing.JComponent.paint(JComponent.java:1065)\r\n        at javax.swing.JLayeredPane.paint(JLayeredPane.java:586)\r\n        at javax.swing.JComponent.paintChildren(JComponent.java:889)\r\n        at javax.swing.JComponent.paintToOffscreen(JComponent.java:5226)\r\n        at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1572)\r\n        at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1495)\r\n        at javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:306)\r\n        at javax.swing.RepaintManager.paint(RepaintManager.java:1265)\r\n        at javax.swing.JComponent.paint(JComponent.java:1042)\r\n        at java.awt.GraphicsCallback$PaintCallback.run(GraphicsCallback.java:39)\r\n        at sun.awt.SunGraphicsCallback.runOneComponent(SunGraphicsCallback.java:79)\r\n        at sun.awt.SunGraphicsCallback.runComponents(SunGraphicsCallback.java:116)                                                                                                 \r\n        at java.awt.Container.paint(Container.java:1973)                                                                                                                           \r\n        at java.awt.Window.paint(Window.java:3912)                                                                                                                                 \r\n        at javax.swing.RepaintManager$4.run(RepaintManager.java:835)                                                                                                               \r\n        at javax.swing.RepaintManager$4.run(RepaintManager.java:807)                                                                                                               \r\n        at java.security.AccessController.doPrivileged(Native Method)                                                                                                              \r\n        at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)                                                                                      \r\n        at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:807)                                                                                                   \r\n        at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:782)                                                                                                   \r\n        at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:731)                                                                                                \r\n        at javax.swing.RepaintManager.access$1300(RepaintManager.java:64)                                                                                                          \r\n        at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1720)                                                                                             \r\n        at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)\r\n        at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)\r\n        at java.awt.EventQueue.access$500(EventQueue.java:97)\r\n        at java.awt.EventQueue$3.run(EventQueue.java:709)\r\n        at java.awt.EventQueue$3.run(EventQueue.java:703)\r\n        at java.security.AccessController.doPrivileged(Native Method)\r\n        at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)\r\n        at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)\r\n        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)\r\n        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)\r\n        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)\r\n        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)\r\n        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)\r\n        at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)\r\nERROR [2016-04-07 11:13:31,713]  [DefaultExceptionHandler.java:49] [AWT-EventQueue-0]  Unhandled exception\r\njava.lang.NullPointerException\r\n        at org.broad.igv.ui.panel.ZoomSliderPanel.paintHorizontal(ZoomSliderPanel.java:182)\r\n        at org.broad.igv.ui.panel.ZoomSliderPanel.paintComponent(ZoomSliderPanel.java:114)\r\n        at javax.swing.JComponent.paint(JComponent.java:1056)\r\n        at javax.swing.JComponent.paintChildren(JComponent.java:889)\r\n        at javax.swing.JComponent.paint(JComponent.java:1065)\r\n        at javax.swing.JComponent.paintChildren(JComponent.java:889)\r\n        at javax.swing.JComponent.paint(JComponent.java:1065)\r\n        at javax.swing.JComponent.paintChildren(JComponent.java:889)\r\n        at javax.swing.JComponent.paint(JComponent.java:1065)\r\n        at javax.swing.JComponent.paintChildren(JComponent.java:889)\r\n        at javax.swing.JComponent.paint(JComponent.java:1065)\r\n        at javax.swing.JLayeredPane.paint(JLayeredPane.java:586)\r\n        at javax.swing.JComponent.paintChildren(JComponent.java:889)\r\n        at javax.swing.JComponent.paintToOffscreen(JComponent.java:5226)\r\n        at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1572)\r\n        at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1495)\r\n        at javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:306)\r\n        at javax.swing.RepaintManager.paint(RepaintManager.java:1265)\r\n        at javax.swing.JComponent.paint(JComponent.java:1042)\r\n        at java.awt.GraphicsCallback$PaintCallback.run(GraphicsCallback.java:39)\r\n        at sun.awt.SunGraphicsCallback.runOneComponent(SunGraphicsCallback.java:79)\r\n        at sun.awt.SunGraphicsCallback.runComponents(SunGraphicsCallback.java:116)\r\n        at java.awt.Container.paint(Container.java:1973)\r\n        at java.awt.Window.paint(Window.java:3912)\r\n        at javax.swing.RepaintManager$4.run(RepaintManager.java:835)\r\n        at javax.swing.RepaintManager$4.run(RepaintManager.java:807)\r\n        at java.security.AccessController.doPrivileged(Native Method)\r\n        at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)\r\n        at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:807)\r\n        at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:782)\r\n        at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:731)\r\n        at javax.swing.RepaintManager.access$1300(RepaintManager.java:64)\r\n        at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1720)\r\n        at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)\r\n        at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)\r\n        at java.awt.EventQueue.access$500(EventQueue.java:97)\r\n        at java.awt.EventQueue$3.run(EventQueue.java:709)\r\n        at java.awt.EventQueue$3.run(EventQueue.java:703)\r\n        at java.security.AccessController.doPrivileged(Native Method)\r\n        at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)\r\n        at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)\r\n        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)\r\n        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)\r\n        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)\r\n        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)\r\n        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)\r\n        at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)\r\n`\r\n\r\nI attached the screenshot of the application display.\r\n![igv error](https://cloud.githubusercontent.com/assets/1442522/14338552/c1c6e33e-fcb2-11e5-8fe7-32779961b6ae.png)\r\n\r\nMy Java environtment is version 1.8.0_45 and support 64-bit.\r\n"},"comment":{"url":"https://api.github.com/repos/igvteam/igv/issues/comments/206937230","html_url":"https://github.com/igvteam/igv/issues/221#issuecomment-206937230","issue_url":"https://api.github.com/repos/igvteam/igv/issues/221","id":206937230,"user":{"login":"jrobinso","id":933148,"avatar_url":"https://avatars.githubusercontent.com/u/933148?v=3","gravatar_id":"","url":"https://api.github.com/users/jrobinso","html_url":"https://github.com/jrobinso","followers_url":"https://api.github.com/users/jrobinso/followers","following_url":"https://api.github.com/users/jrobinso/following{/other_user}","gists_url":"https://api.github.com/users/jrobinso/gists{/gist_id}","starred_url":"https://api.github.com/users/jrobinso/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jrobinso/subscriptions","organizations_url":"https://api.github.com/users/jrobinso/orgs","repos_url":"https://api.github.com/users/jrobinso/repos","events_url":"https://api.github.com/users/jrobinso/events{/privacy}","received_events_url":"https://api.github.com/users/jrobinso/received_events","type":"User","site_admin":false},"created_at":"2016-04-07T14:45:41Z","updated_at":"2016-04-07T14:45:41Z","body":"The log indicated an attempt to load the .fai file directly.  I'm going to reopen this ticket as a reminder to add a check for that,  we should be able to detect it and give an error."}}