igv: IGV won't start anymore on Mac

Hi, I was running IGV just fine until yesterday, when it started running away with CPU usage, and then after force quitting, it won’t launch again. I’ve tried deleting all the relevant files, reinstalling etc and to no avail. I’ve tried launching it with Java 14 as well as Java 11…

Here’s my error message: `WARN [2021-02-03T12:24:08,520] [Globals.java:135] [main] Development mode is enabled INFO [2021-02-03T12:24:08,536] [DirectoryManager.java:180] [main] IGV Directory: /Users//igv INFO [2021-02-03T12:24:09,657] [Main.java:205] [AWT-EventQueue-0] Startup IGV Version 2.9.0 02/01/2021 06:00 PM INFO [2021-02-03T12:24:09,675] [Main.java:206] [AWT-EventQueue-0] Java 11.0.9 (build 11.0.9+11) 2020-10-20 INFO [2021-02-03T12:24:09,676] [Main.java:209] [AWT-EventQueue-0] Java Vendor: Oracle Corporation https://openjdk.java.net/ INFO [2021-02-03T12:24:09,677] [Main.java:211] [AWT-EventQueue-0] JVM: OpenJDK 64-Bit Server VM
INFO [2021-02-03T12:24:09,849] [Main.java:214] [AWT-EventQueue-0] Default User Directory: /Users/
INFO [2021-02-03T12:24:09,850] [Main.java:215] [AWT-EventQueue-0] OS: Mac OS X 10.15.5 x86_64 ERROR [2021-02-03T12:24:10,156] [DefaultExceptionHandler.java:49] [AWT-EventQueue-0] Unhandled exception java.lang.NullPointerException: null at org.broad.igv.util.AmazonUtils.GetCognitoAWSCredentials(AmazonUtils.java:101) ~[igv.jar:?] at org.broad.igv.util.AmazonUtils.createPresignedURL(AmazonUtils.java:408) ~[igv.jar:?] at org.broad.igv.util.AmazonUtils.translateAmazonCloudURL(AmazonUtils.java:438) ~[igv.jar:?] at org.broad.igv.util.HttpUtils.mapURL(HttpUtils.java:146) ~[igv.jar:?] at org.broad.igv.util.HttpUtils.createURL(HttpUtils.java:135) ~[igv.jar:?] at org.broad.igv.util.HttpUtils.resourceAvailable(HttpUtils.java:335) ~[igv.jar:?] at org.broad.igv.util.FileUtils.resourceExists(FileUtils.java:56) ~[igv.jar:?] at org.broad.igv.ui.commandbar.GenomeListManager.getUserDefinedGenomeMap(GenomeListManager.java:453) ~[igv.jar:?] at org.broad.igv.ui.commandbar.GenomeListManager.rebuildGenomeItemMap(GenomeListManager.java:84) ~[igv.jar:?] at org.broad.igv.ui.commandbar.GenomeListManager.getGenomeItemMap(GenomeListManager.java:72) ~[igv.jar:?] at org.broad.igv.ui.commandbar.GenomeComboBox.getModelForGenomeListComboBox(GenomeComboBox.java:66) ~[igv.jar:?] at org.broad.igv.ui.commandbar.GenomeComboBox.refreshGenomeListComboBox(GenomeComboBox.java:40) ~[igv.jar:?] at org.broad.igv.ui.commandbar.IGVCommandBar.lambda$refreshGenomeListComboBox$1(IGVCommandBar.java:212) ~[igv.jar:?] at org.broad.igv.ui.util.UIUtilities.invokeAndWaitOnEventThread(UIUtilities.java:166) ~[igv.jar:?] at org.broad.igv.ui.commandbar.IGVCommandBar.refreshGenomeListComboBox(IGVCommandBar.java:211) ~[igv.jar:?] at org.broad.igv.ui.commandbar.IGVCommandBar.<init>(IGVCommandBar.java:103) ~[igv.jar:?] at org.broad.igv.ui.IGVContentPane.<init>(IGVContentPane.java:73) ~[igv.jar:?] at org.broad.igv.ui.IGV.<init>(IGV.java:245) ~[igv.jar:?] at org.broad.igv.ui.IGV.createInstance(IGV.java:147) ~[igv.jar:?] at org.broad.igv.ui.Main.open(Main.java:341) ~[igv.jar:?] at org.broad.igv.ui.Main.lambda$main$0(Main.java:118) ~[igv.jar:?] at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313) ~[?:?] at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770) ~[?:?] at java.awt.EventQueue$4.run(EventQueue.java:721) ~[?:?] at java.awt.EventQueue$4.run(EventQueue.java:715) ~[?:?] at java.security.AccessController.doPrivileged(Native Method) ~[?:?] at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85) ~[?:?] at java.awt.EventQueue.dispatchEvent(EventQueue.java:740) ~[?:?] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) [?:?] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) [?:?] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) [?:?] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) [?:?] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [?:?] at java.awt.EventDispatchThread.run(EventDispatchThread.java:90) [?:?] INFO [2021-02-03T12:24:11,170] [ShutdownThread.java:47] [Thread-1] Shutting down

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About this issue

  • Original URL
  • State: closed
  • Created 3 years ago
  • Comments: 18 (12 by maintainers)

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Sorry for the slow reply, @jrobinso I removed the “user-defined-genomes.txt” file and now it works! Thanks for the help.