Jalview has encountered an error during launch

If you’ve been redirected to this FAQ then it probably means that the Jalview Native application has encountered an error whilst trying to start. Here are some tips for various problems:

Problems on Windows:

If your installation of Jalview goes fine, but double clicking on the Jalview icon does not produce any error message, window or any other activity (other than the spinning blue circle) this might be caused by a space character in Jalview’s installation folder. To fix this:

  1. Uninstall the non-working Jalview by either: * Open the Control Panel and go to Programs→Programs and Features→Uninstall a program. Select Jalview from the program list and then click on the Uninstall/Change button above the list. This will launch Jalview’s uninstall wizard, follow the instructions. * Open a File Explorer and go to location %APPDATA%\Local\Jalview\uninstall.exe or %LOCALAPPDATA%\Local\Jalview\uninstall.exe if the first one isn’t found. This should launch Jalview’s uninstall wizard, follow the instructions.
  2. Install Jalview again using the same installer as before, but this time on the second screen (Select Destination Directory) ensure the path has no spaces (e.g. type in C:\Jalview)

Problems on linux:

  1. If you have used the Jalview-X_unix_installer_x_x_x-j8.sh installer, or the similar *-j8.tar.gz distribution, in some cicumstances you might get an error when launching Jalview that includes the message “Failed to rename ./jre.tgz_new to ./jre.tgz”:

This (slightly misleading) error message is caused by the launcher not being able to find the right version of the Java runtime environment (JRE).

For Jalview or later we distribute an installer for linux with 64bit intel processors that bundles a JRE, we recommend using this installer to upgrade. For other linux platforms please read below.

In the case of Jalview 2.11.0 this should be Java 1.8. You can fix this by installing the right version of Java either with your distribution’s package manager. e.g.

On Ubuntu 18.04:

sudo apt install openjdk-8-jre

On CentOS 8 or Fedora 31:

sudo yum install java-1.8.0-openjdk

or you can install a local version of the Java runtime environment – we recommend the installers from AdoptOpenJDK.

If after installing a Java 1.8 runtime environment you are experiencing the same problem, you may need to tell the Jalview launcher where to find the JRE 1.8 with the environment variable INSTALL4J_JAVA_HOME_OVERRIDE. You can achieve this on the command line with, e.g. (assuming you installed Jalview in the default location ~/opt/Jalview)

On Ubuntu 18.04,

INSTALL4J_JAVA_HOME_OVERRIDE=/usr/lib/jvm/java-8-openjdk-amd64 ~/opt/Jalview/Jalview

On CentOS 8 or Fedora 31

INSTALL4J_JAVA_HOME_OVERRIDE=/usr/lib/jvm/jre-1.8.0 ~/opt/Jalview/Jalview

Alternatively you could add an “export INSTALL4J_JAVA_HOME_OVERRIDE=…” in your ~/.bashrc file but this could affect other applications installed using install4j.

Jalview will use a Java 11 runtime environment in version 2.12.

  1. If you have the openjdk-8-jre-headless package installed but NOT the openjdk-8-jre package (for example this might be default on an Ubuntu Server distribution) then you might find Jalview silently fails to launch and the ~/opt/Jalview/launcher.log file contains:
Exception in thread "Getdown" java.awt.AWTError: Assistive Technology not found: org.GNOME.Accessibility.AtkWrapper

To fix this you can either install openjdk-8-java with

sudo apt install openjdk-8-java

or comment out the following line “assistive_technologies=org.GNOME.Accessibility.AtkWrapper” in the file /etc/java-8-openjdk/accessibility.properties. You can do this with

sudo sed -i -E 's/^(assistive_technologies=org\.GNOME\.Accessibility\.AtkWrapper)/#\1/' /etc/java-8-openjdk/accessibility.properties

Other problems:

Depending on your platform you will need to take a look at the launcher.log file within the Jalview installation directory:

  • On Windows the Jalview installation directory defaults to %APPDATA%\Local\Jalview,
  • On Linux/Unix the Jalview installation directory defaults to ~/opt/Jalview,
  • On macOS the launcher.log file can be found in /Applications/Jalview.app/Contents/Resources/app. To get here in Finder right click on the Jalview icon in Applications and select “Show Package Contents”. You can then click through to Contents → Resources→ app . Warning! Editing or deleting files in the Jalview.app package might result in your Jalview installation breaking!