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
I love Artemis and I need to to work!
Please advice me to fix this error.
I have installed artemis both via terminal and also by downloading the dmg.
I've tried JDK 19 and JDK 21 (the latest version).
It runs but when trying to use Edit -> subsequence (and features) it freezes and nothing happens. I suspect it has something to do with Java. Otherwise it seems as if artemis is working fine.
This is whats prompted in the terminal:
art
Starting Artemis with arguments: -mx2g -ms100m -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 -Dapple.laf.useScreenMenuBar=true -Xdock:name=Artemis
Warning: the fonts "Times" and "Times" are not available for the Java logical font "Serif", which may have unexpected appearance or behavior. Re-enable the "Times" font to remove this warning.
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at uk.ac.sanger.artemis.Entry.add(Entry.java:589)
at uk.ac.sanger.artemis.Entry.add(Entry.java:536)
at uk.ac.sanger.artemis.Entry.truncate(Entry.java:880)
at uk.ac.sanger.artemis.SimpleEntryGroup.truncate(SimpleEntryGroup.java:1031)
at uk.ac.sanger.artemis.components.EditMenu.editSubSequence(EditMenu.java:1083)
at uk.ac.sanger.artemis.components.EditMenu.access$400(EditMenu.java:70)
at uk.ac.sanger.artemis.components.EditMenu$5.actionPerformed(EditMenu.java:351)
at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1967)
at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2308)
at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:405)
at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262)
at java.desktop/javax.swing.AbstractButton.doClick(AbstractButton.java:369)
at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1020)
at java.desktop/com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1064)
at java.desktop/java.awt.Component.processMouseEvent(Component.java:6635)
at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3342)
at java.desktop/java.awt.Component.processEvent(Component.java:6400)
at java.desktop/java.awt.Container.processEvent(Container.java:2263)
at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:5011)
at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2321)
at java.desktop/java.awt.Component.dispatchEvent(Component.java:4843)
at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4918)
at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4547)
at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4488)
at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2307)
at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2772)
at java.desktop/java.awt.Component.dispatchEvent(Component.java:4843)
at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:772)
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.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:95)
at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745)
at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:743)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:742)
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)
Hi,
I love Artemis and I need to to work! Please advice me to fix this error.
I have installed artemis both via terminal and also by downloading the dmg. I've tried JDK 19 and JDK 21 (the latest version).
It runs but when trying to use Edit -> subsequence (and features) it freezes and nothing happens. I suspect it has something to do with Java. Otherwise it seems as if artemis is working fine.
This is whats prompted in the terminal: art Starting Artemis with arguments: -mx2g -ms100m -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 -Dapple.laf.useScreenMenuBar=true -Xdock:name=Artemis Warning: the fonts "Times" and "Times" are not available for the Java logical font "Serif", which may have unexpected appearance or behavior. Re-enable the "Times" font to remove this warning. Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at uk.ac.sanger.artemis.Entry.add(Entry.java:589) at uk.ac.sanger.artemis.Entry.add(Entry.java:536) at uk.ac.sanger.artemis.Entry.truncate(Entry.java:880) at uk.ac.sanger.artemis.SimpleEntryGroup.truncate(SimpleEntryGroup.java:1031) at uk.ac.sanger.artemis.components.EditMenu.editSubSequence(EditMenu.java:1083) at uk.ac.sanger.artemis.components.EditMenu.access$400(EditMenu.java:70) at uk.ac.sanger.artemis.components.EditMenu$5.actionPerformed(EditMenu.java:351) at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1967) at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2308) at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:405) at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262) at java.desktop/javax.swing.AbstractButton.doClick(AbstractButton.java:369) at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1020) at java.desktop/com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1064) at java.desktop/java.awt.Component.processMouseEvent(Component.java:6635) at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3342) at java.desktop/java.awt.Component.processEvent(Component.java:6400) at java.desktop/java.awt.Container.processEvent(Container.java:2263) at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:5011) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2321) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4843) at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4918) at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4547) at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4488) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2307) at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2772) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4843) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:772) 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.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:95) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:743) at java.base/java.security.AccessController.doPrivileged(Native Method) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:742) 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)
Thank you in advance!