HomeCLC FAQ - Basics: Installation, data, system resourcesStarting up and running the WorkbenchWhy is my Workbench taking so long to start up?

4.2. Why is my Workbench taking so long to start up?

There are a few common reasons why you a CLC Workbench can take a long time to start up.  These include:

  1. Something associated with your user settings is the source of the problem.
  2. The default Data Location is a shortcut.
  3. Anti-virus software is scanning the software.


User settings

Commonly associated with the message "Loading Settings" in the startup screen.

If a CLC Workbench stalls on startup, and you can see the text: "Loading Settings" in the startup screen, then it suggests that something has happened to your user settings. This can involve things like particular view settings you have saved, or the data objects that were open when you quit the Workbench and are now being loaded again on startup.

The first thing to try to resolve this issue is to locate and move your current user settings file, usersettings.xml. When this file is no longer where the Workbench expects it to be, then it will copy that file from an older version of the Workbench, if you had one installed, or will re-create that file anew if it cannot find an older version to copy from.


  • If the Workbench is still attempting to start up, please kill that process.
  • Please find the usersettings.xml file for the latest version of the Workbench you are having trouble starting up.
  • Move that to another location on your machine. Information about where to find this file is included in the related page linked below.
  • Start up your Workbench.

If a particular data object being opened was the cause of the issue, then these actions should have solved the problem. The downside of the above process is that if you have saved customized view settings for particular types of data objects, these will be lost unless they were already saved in the next-to-latest version of the Workbench that you have run on your machine.


If the problem also existed is in a user setting file from a previous version of the Workbench, the above actions will not resolve the problem. In this case, please remove, or move to another location on your system, the folders containing the user settings for all your Workbenches and versions and then try starting up your Workbench again. Please note that this action will mean that any special viewing settings you have saved in the past will not be present in the Workbench when it starts up.


Shortcut to default Data Location

Commonly associated with the message "Loading Editors" in the startup screen.

The Workbench may stall during startup with the startup splash screen and the text 'Loading Editors' in view.

In this case, please check that the default Workbench Data Location is not a shortcut or a symbolic or hard link to another location on your filesystem. Unless changed, the CLC Workbench default Data Location will be associated with a subfolder called "CLC_Data" under your home area on the computer. Please ensure this, or the folder you have set as the default Data Location, is not a short cut or link.

Anti-virus software

Anti-virus software configured to run on-access scanning can cause a substantial delay in the start-up of the Workbench in cases where the software carries out archive scanning. As a java-based program the Genomics Workbench makes extensive use of jar files, which are (correctly) considered archives by the on-access scanner.

The solution to the issue of a long start-up time for the Workbench would generally involve modifying the configuration of the on-access scanning software. Possible solutions could include configuring the software such that the CLC Genomics Workbench installation directory, and its subdirectories, are excluded from the areas that the scanner should be checking. Alternatively, all jar files within the CLC Genomics Workbench installation directory, and its subdirectories could be part of an exclude list. (In this case, this list will then need to be verified each time the Workbench is updated.) You will likely need to discuss the options possible at your site with your local IT administrators or IT security organization.


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