Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
Starting Artemis with arguments: -mx10g -ms2g -noverify --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED -Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX
Exception in thread "AWT-EventQueue-0" java.lang.InternalError: java.lang.reflect.InvocationTargetException
at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
at java.desktop/sun.swing.SwingUtilities2.getFontMetrics(SwingUtilities2.java:1231)
at java.desktop/javax.swing.JComponent.getFontMetrics(JComponent.java:1646)
at java.desktop/javax.swing.plaf.basic.BasicGraphicsUtils.getPreferredButtonSize(BasicGraphicsUtils.java:351)
at java.desktop/javax.swing.plaf.basic.BasicButtonUI.getPreferredSize(BasicButtonUI.java:474)
at java.desktop/javax.swing.JComponent.getPreferredSize(JComponent.java:1680)
at java.desktop/java.awt.FlowLayout.preferredLayoutSize(FlowLayout.java:414)
at java.desktop/java.awt.Container.preferredSize(Container.java:1823)
at java.desktop/java.awt.Container.getPreferredSize(Container.java:1807)
at java.desktop/javax.swing.JComponent.getPreferredSize(JComponent.java:1682)
at java.desktop/java.awt.BorderLayout.preferredLayoutSize(BorderLayout.java:734)
at java.desktop/java.awt.Container.preferredSize(Container.java:1823)
at java.desktop/java.awt.Container.getPreferredSize(Container.java:1807)
at java.desktop/javax.swing.JComponent.getPreferredSize(JComponent.java:1682)
at java.desktop/javax.swing.JRootPane$RootLayout.preferredLayoutSize(JRootPane.java:866)
at java.desktop/java.awt.Container.preferredSize(Container.java:1823)
at java.desktop/java.awt.Container.getPreferredSize(Container.java:1807)
at java.desktop/javax.swing.JComponent.getPreferredSize(JComponent.java:1682)
at java.desktop/java.awt.BorderLayout.preferredLayoutSize(BorderLayout.java:724)
at java.desktop/java.awt.Container.preferredSize(Container.java:1823)
at java.desktop/java.awt.Container.getPreferredSize(Container.java:1807)
at java.desktop/java.awt.Window.pack(Window.java:826)
at uk.ac.sanger.artemis.components.FileViewer.(FileViewer.java:265)
at uk.ac.sanger.artemis.components.FileViewer.(FileViewer.java:122)
at uk.ac.sanger.artemis.components.FileViewer.(FileViewer.java:115)
at uk.ac.sanger.artemis.components.LogViewer$1.(LogViewer.java:92)
at uk.ac.sanger.artemis.components.LogViewer.maybeMakeViewer(LogViewer.java:91)
at uk.ac.sanger.artemis.components.LogViewer.log(LogViewer.java:61)
at uk.ac.sanger.artemis.components.Splash.initLogger(Splash.java:252)
at uk.ac.sanger.artemis.components.Splash.(Splash.java:147)
at uk.ac.sanger.artemis.components.Splash.(Splash.java:173)
at uk.ac.sanger.artemis.components.ArtemisMain.(ArtemisMain.java:78)
at uk.ac.sanger.artemis.components.ArtemisMain$10.run(ArtemisMain.java:793)
at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
Caused by: java.lang.reflect.InvocationTargetException
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
... 49 more
Caused by: java.lang.NullPointerException
at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.desktop/sun.font.SunFontManager.(SunFontManager.java:312)
at java.desktop/sun.awt.FcFontManager.(FcFontManager.java:35)
at java.desktop/sun.awt.X11FontManager.(X11FontManager.java:56)
... 54 more
openjdk 11.0.1 2018-10-16 LTS
OpenJDK Runtime Environment Zulu11.2+3 (build 11.0.1+13-LTS)
OpenJDK 64-Bit Server VM Zulu11.2+3 (build 11.0.1+13-LTS, mixed mode)
artemis installed via conda (the latest one)
could anyone tell me what went wrong? it used to work few weeks ago (maybe before conda upgrading)
Starting Artemis with arguments: -mx10g -ms2g -noverify --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED -Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX(FileViewer.java:265)
at uk.ac.sanger.artemis.components.FileViewer.(FileViewer.java:122)
at uk.ac.sanger.artemis.components.FileViewer.(FileViewer.java:115)
at uk.ac.sanger.artemis.components.LogViewer$1.(LogViewer.java:92)
at uk.ac.sanger.artemis.components.LogViewer.maybeMakeViewer(LogViewer.java:91)
at uk.ac.sanger.artemis.components.LogViewer.log(LogViewer.java:61)
at uk.ac.sanger.artemis.components.Splash.initLogger(Splash.java:252)
at uk.ac.sanger.artemis.components.Splash.(Splash.java:147)
at uk.ac.sanger.artemis.components.Splash.(Splash.java:173)
at uk.ac.sanger.artemis.components.ArtemisMain.(ArtemisMain.java:78)
at uk.ac.sanger.artemis.components.ArtemisMain$10.run(ArtemisMain.java:793)
at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
Caused by: java.lang.reflect.InvocationTargetException
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
... 49 more
Caused by: java.lang.NullPointerException
at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.desktop/sun.font.SunFontManager.(SunFontManager.java:312)
at java.desktop/sun.awt.FcFontManager.(FcFontManager.java:35)
at java.desktop/sun.awt.X11FontManager.(X11FontManager.java:56)
... 54 more
Exception in thread "AWT-EventQueue-0" java.lang.InternalError: java.lang.reflect.InvocationTargetException at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86) at java.base/java.security.AccessController.doPrivileged(Native Method) at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74) at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247) at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265) at java.desktop/sun.swing.SwingUtilities2.getFontMetrics(SwingUtilities2.java:1231) at java.desktop/javax.swing.JComponent.getFontMetrics(JComponent.java:1646) at java.desktop/javax.swing.plaf.basic.BasicGraphicsUtils.getPreferredButtonSize(BasicGraphicsUtils.java:351) at java.desktop/javax.swing.plaf.basic.BasicButtonUI.getPreferredSize(BasicButtonUI.java:474) at java.desktop/javax.swing.JComponent.getPreferredSize(JComponent.java:1680) at java.desktop/java.awt.FlowLayout.preferredLayoutSize(FlowLayout.java:414) at java.desktop/java.awt.Container.preferredSize(Container.java:1823) at java.desktop/java.awt.Container.getPreferredSize(Container.java:1807) at java.desktop/javax.swing.JComponent.getPreferredSize(JComponent.java:1682) at java.desktop/java.awt.BorderLayout.preferredLayoutSize(BorderLayout.java:734) at java.desktop/java.awt.Container.preferredSize(Container.java:1823) at java.desktop/java.awt.Container.getPreferredSize(Container.java:1807) at java.desktop/javax.swing.JComponent.getPreferredSize(JComponent.java:1682) at java.desktop/javax.swing.JRootPane$RootLayout.preferredLayoutSize(JRootPane.java:866) at java.desktop/java.awt.Container.preferredSize(Container.java:1823) at java.desktop/java.awt.Container.getPreferredSize(Container.java:1807) at java.desktop/javax.swing.JComponent.getPreferredSize(JComponent.java:1682) at java.desktop/java.awt.BorderLayout.preferredLayoutSize(BorderLayout.java:724) at java.desktop/java.awt.Container.preferredSize(Container.java:1823) at java.desktop/java.awt.Container.getPreferredSize(Container.java:1807) at java.desktop/java.awt.Window.pack(Window.java:826) at uk.ac.sanger.artemis.components.FileViewer.
openjdk 11.0.1 2018-10-16 LTS OpenJDK Runtime Environment Zulu11.2+3 (build 11.0.1+13-LTS) OpenJDK 64-Bit Server VM Zulu11.2+3 (build 11.0.1+13-LTS, mixed mode)
artemis installed via conda (the latest one)
could anyone tell me what went wrong? it used to work few weeks ago (maybe before conda upgrading)
many thanks