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CLC FAQ - Basics: Installation, data, system resources
- 1. Installation and upgrades
- 1.1. Where can I get installer files for the software?
- 1.2. What Linux distributions do you support?
- 1.3. How can I install the CLC Workbench on a Linux system using the installer script?
- 1.4. How can I upgrade my CLC Workbench?
- 1.5. Where should I install an upgrade to my CLC Workbench software?
- 1.6. Where should I install an upgrade to my CLC Server software?
- 1.7. Can I install a CLC Genomics Workbench on a compute cluster?
- 1.8. How do I install or upgrade my Workbench on a non-networked machine?
- 1.9. How can I uninstall a CLC Workbench?
- 1.10. How do I download the software if I get a message about the signature being corrupt or invalid?
- 1.11. What does "error code 34" mean when I run the installer?
- 1.12. How can I get a copy of the SDK?
- 1.13. What does it mean if a Mac installer says it "is damaged and can't be opened"?
- 2. Data and files
- 2.1. Where are the Workbench logfiles?
- 2.2. Where is my user settings file?
- 2.3. Where is my CLC Workbench data?
- 2.4. How can I add a new data location to the Navigation Area?
- 2.5. How can I set a different default location for data to be saved into?
- 2.6. How can I move my CLC data?
- 2.7. Where are my temporary files to be written to and how can I change this?
- 2.8. Where is my Workbench installation directory?
- 2.9. Why is my data location greyed out in the Workbench navigation area?
- 2.10. Why are temporary files still written to the old default location after I redirect them?
- 2.11. What does an error about problems writing to temp mean?
- 2.12. How can I delete a whole data location and all its contents?
- 3. System and resources
- 3.1. What is the difference between running a Genomics Server and running a Genomics Workbench on a large central machine that multiple users can access?
- 3.2. Are the tools of the CLC Workbenches or Servers multi-threaded?
- 3.3. How do I change the memory limit for the CLC Workbench or Server java process?
- 3.4. Can I limit the number of CPUs used by a CLC Workbench?
- 3.5. Why is the Workbench/Server holding onto memory between jobs?
- 3.6. Which internet addresses does CLC software need access to?
- 3.7. Why does the Workbench 3D Viewer throw a OpenGL error suggeting that my graphics card needs updating?
- 3.8. Will a high spec graphics card improve CLC Workbench performance?
- 3.9. Can I run CLC Workbench software on a machine that is not network connected?
- 4. Starting up and running the Workbench
- 4.1. Which tasks require me to run the Workbench as an administrative user and how?
- 4.2. Why is my Workbench taking so long to start up?
- 4.3. Why can't I see the Workbench even though it is running on my Windows system?
- 4.4. Why do I see a JVM error when I start up the Workbench?
- 4.5. Why is the Workbench sometimes slow on OS X Mavericks and later versions?
- 5. Plugins
- 6. Documentation
1. Installation and upgrades
1.1. Where can I get installer files for the software?
There are a number of ways you can get installer files for CLC software. These are:
- Via your myCLC account (current and older versions of the software)
- Via the CLC bio website (latest version of the software only)
Plugin installers are provided separately, as described at the bottom of this FAQ entry.
Getting installer files via your myCLC account
Installer files for the current releases as well as older versions of CLC core products can be downloaded via your myCLC account.
If your license for your CLC software product is presently covered under our maintenance, upgrades, and support (MUS) program
- Log into your myCLC account.
- Click on the Download tab on the right hand side of the page. You should now see listed the products you have licenses for.
- In the drop-down list, the most recent version of the software you are eligible to run should be the version selected by default.
- Click on the Download link for the installer file appropriate to the operating system you will run the software on.
If your license for your CLC software product is not covered under our maintenance, upgrades, and support (MUS) program
- Log into your myCLC account.
- Click on the Licenses tab on the right hand side of the page. You should now see listed the products you have licenses for.
- Under Active licenses with expired maintenance section, click on the plus symbol to the left of the product in question to expand that section.
- Under the subsection called Products, click on the name of the product. This will take you directly to a page of download links for installers for a version of the software compatible with your license.
Please note that if you have multiple licenses for a product, where some are covered by the MUS program and some are not, then you will be shown the installer files for the latest version of the software, even if you selected a license that was no longer covered. In this case, please select the latest version supported by your license from the drop down list of version numbers.
If you are using licenses owned by someone else
- Log into your myCLC account.
- Click on the Downloads tab on the right hand side of the page.
- Click on the More CLC Products tab within the Downloads tab section.
- Find the product you need in the list and select the version you need installers for using the drop down menu beside the relevant product name.
If you do not already have access to your myCLC account, a linked page from this FAQ provides information on how to request this.
The latest version of CLC core products are available from our website.
You can navigate to individual product webpages from
https://digitalinsights.qiagen.com/products/ Where relevant, software installers can be downloaded from such product webpages. Installer files made available this way are always for the latest version of the software.
Getting plugin installers
Plugins for CLC Workbenches can be downloaded and installed via the Plugin Manager of that software.
Plugin installers for both CLC Workbenches and CLC Servers can be downloaded from our website at:
Just click on the Download icon (a downwards facing arrow on the right hand side) for the relevant plugin and then choose the installer matching the core product version you are using.
1.2. What Linux distributions do you support?
The Linux distributions we officially support are listed for each software application on our system requirements webpage:
We also expect that CLC software should install and run on most standard Linux distributions. Besides the systems listed as supported, we are aware of our software being run successfully on CentOS, Arch Linux, Mandriva, and Debian, along with Debian-based derivatives such as Ubuntu and Mint. We cannot guarantee that issues will not arise on particular Linux systems that we do not officially support, but we do not anticipate problems.
Instructions for using the Linux .sh installation scripts for installing Workbenches can be found via the Related page links at the bottom of this page. Installation instructions can also be found in the relevant product manuals.
1.3. How can I install the CLC Workbench on a Linux system using the installer script?
These instructions are written for the 64 bit Linux installer script for CLC Genomics Workbench (which is a file with a name that ends in .sh) The instructions are the same for installation using the the 32 bit version, or for other Workbench versions. The only differences is the specific installation script name..
Please download the relevant Linux installer file if you have not already. This is a file that ends in .sh (not the rpm package).
Information about where to download installers for the software is in the FAQ page: Where can I get installer files for the software?
To install to a central location on your system, please run the installation script you have downloaded as an administrative user. For version 6.0.2 of the Genomics Workbench on a 64 bit linux system, this would be done by typing this command:
sudo /bin/sh CLCGenomicsWorkbench_6_0_2_64.sh
If you do not have sudo privileges on your system, you can just type this command:
If you ran the command with sudo, then choose a central location to install to. A common choice might be:
but you are free to install wherever makes sense on your system.
If you did not run the command with sudo, then you will need to install somewhere under your own home area.
If you ran the command with sudo, then you can chose to set up symlinks, and let them be made in /usr/local/bin. This is not mandatory. If you didn't run the installer with sudo, then you won't have permission to do this anyway.
When you get to the end of the installation process, it will probably ask if you'd like to start up the workbench. Please note that if you choose to do this and you ran the installation script using sudo, then this will start up the Workbench as the root user. While you are running the workbench, you can set up your license. You can also then click on the Plugins button and download and install plugins you want.
If you were running the installer with sudo, then quit the workbench after you've sorted out the license and any plugins you want. Then restart the workbench (without using sudo). If you were not using sudo, then you can continue to work with the Workbench at this point.
1.4. How can I upgrade my CLC Workbench?
Instructions are provided below for upgrading to a new minor version of the software (e.g. 11.0 to 11.0.1) and for upgrading between major version lines (e.g. 11.x to 12.x).
Relevant related FAQ entries include:
- Where can I get installer files for the software?
- How do I run the Workbench as administrative user?
- Where should I install an upgrade to my CLC Workbench software?
- How do I install or upgrade my Workbench on a non-networked machine?
- What are the license details for the CLC software I am using?
- How do I get a new static license when upgrading between major software versions?
Upgrading to a new minor version of the software
Here, you just need to:
- Download an installer file.
- Run the installer file as an administrative user.
When the software is installed, you can close the Workbench and start it up again as a regular user to run your analyses.
Upgrading to a new major version of the software
You are able to upgrade to a new major version if the license you are using is covered by our Maintenance, Upgrades and Support (MUS) program.
To upgrade to a new major version, you will then also need to carry out the following steps:
- Download an installer file.
- Run the installer file as an administrative user.
- Start up the newly installed Workbench as an administrative user.
- Upgrade your license if it is a static license, or configuring your license connection if you are using a network license.
- (optional) Install plugins via the Plugins manager, which is launched from the Plugins button on the toolbar.
Please note that in the case of network licenses, your License Server administrator will need to have downloaded and installed a version of the license that supports the major version line of the Workbench you wish to run.
After your Workbench has the appropriate license set up, you can close the Workbench and start it up again as a regular user to run your analyses.
1.5. Where should I install an upgrade to my CLC Workbench software?
You can install CLC software anywhere on your machine you have appropriate permissions for. The location you choose to install Workbench software does not affect user-specific settings such as configured data areas or viewing settings, as these are held within a user's home area.
Points to consider when upgrading a CLC Workbench installation:
Upgrading within the same major release line
Here it is generally best to upgrade in place. That is, install the new version on top of the existing Workbench installation in that release line. (e.g. version 10.5 of the Genomics Workbench would be installed into the folder where version 10.0 was previously installed.)
When updating CLC Workbenches within a given release line, you will be prompted to specify whether to install to the same folder as you previously installed to, or whether you would like to install to a new location. If you are not sure where you previously installed to and would like to check, then just choose to install to a new location. The old location will appear as the default, and you can then proceed to install to that location if you wish.
Upgrading to a new major version line
Please install the Workbench to a new location. Installing to a new location is the default behavior in this case. Please do not choose to install on top of an existing Workbench in an older release line.
When updating Workbenches of different lines (e.g. Genomics Workbench 10.x when you previously had Genomics Workbench 9.x installed), the default installation location is to a new area. For example, on Linux, the default location for version of the Genomics Workbench in the 9.x line would be something like:
whereas for releases in the 10.x line, it would be
When upgrading to a new major version of the Workbench, you will also need to upgrade your license file. How to do this is described in the manual starting at:
The same license upgrade information pertains to all CLC Workbenches.
To install software to a central location on your system, you will generally have to run the installer as an administrative user. Please see the related FAQ page for how to do this on your system.
"Major version" or "major release line" refers to the first digit in the version number. A minor release or bug fix release refers to the digit after a decimal point in the version. For example:
- CLC Genomics Workbench 10.0.1 and 10.5 are different minor releases in the same major release line. The major release number here is 10.
- CLC Genomics Workbench 9.x is is part of a different major release line than 10.x because the major version number is different (9 versus 10).
1.6. Where should I install an upgrade to my CLC Server software?
Our general recommendation when upgrading CLC Server software is to upgrade in place. Choosing to upgrade in place, that is, to install the new software to the same location as your existing CLC Server software allows your existing settings (e.g. File Locations, Users and Groups configurations, Import/Export directories, BLAST database, and so on) to be retained as these settings are stored under the installation area of the software.
When updating a CLC Server product, you will be prompted to specify whether you want to install to the same folder as your existing installation. If you are not sure where you previously installed to and would like to check, then just choose to install to a new location. The old location will appear as the default, which you can then proceed to install to.
When upgrading to a new major version, you will also need to download your license again. This is described in the Genomics Server manual starting here:
The same information is valid for other CLC Server products.
Some relevant links about Server software installation:
1.7. Can I install a CLC Genomics Workbench on a compute cluster?
- The Genomics Workbench was not designed for the purposes of having multiple users using the same copy of the software at the same time. Thus there is no queuing system built into it. This means that people need to take care when submitting computationally intensive jobs if there are others that might also be working with the Genomics Workbench on the same machine at the same time. Jobs on the CLC Workbench are launched immediately and it would be relatively straightforward to exceed the computer resources available if many computationally intensive jobs were attempted at the same time.
- The Genomics Workbench installation is configured to use an amount of memory that matches the machine used to install the Workbench. Depending on the available memory in machines in the compute cluster this may need modification to match the cluster machines. Please see the related FAQ page linked below.
- Please note that you will almost always need to have access to CLC network licenses if you choose to install and run a CLC Genomics Workbench on a node or nodes of a compute cluster. This is because:
- Remote access is not supported by our static license conditions, and compute cluster nodes are usually machines accessed by users remotely.
- If the compute nodes have more than 64 cores, then network licenses are required for CLC Workbenches.
1.8. How do I install or upgrade my Workbench on a non-networked machine?
CLC Workbench software can be installed on a machine that is not connected to the external network by doing the following:
- Using a machine that is connected to the internet, download the installer file for the CLC Workbench.
Information about how to download the installer file for your Workbench can be found in the related FAQ: Where can I get installer files for the software?
- If you wish to install any of the available Workbench plugins, please download the Workbench plugin files from the plugin page: https://www.qiagenbioinformatics.com/plugins/
The relevant plugin files can be downloaded by clicking the button in the Download column on that page.
- If you are installing this software for the first time or are upgrading to a new major version (e.g. 6.x --> 7.x), then you will need to download a license file for the (non-networked) machine you plan to install the Workbench on. You will need your license order ID and the host ID of the machine the software will be run on for this. Information about how to accomplish this can be found at:
- That information is written for the CLC Genomics Workbench but is relevant for other CLC Workbenches also.
If you are upgrading the Workbench with another version in the same release line, then you do not need to download a license file. As an example, v10.0.x and 10.5.x are in the same major release line, as both have "10" as the first digit, and they can be run using an existing license file that supports the 10.x line.
- Transfer the Workbench installer, plugin files, and the license file to the non-networked machine you wish to install the software on. This would usually be done by saving to an area accessible to that machine, or by saving the files to a USB stick or other form of portable storage available to you and loading them onto a non-networked machine.
- Run the Workbench installer as an administrative user on the non-networked machine.
- Once the software is installed, start up the Workbench as an administrative user.
- If you have downloaded a license file (step 3) or you have chosen to install a minor update to a new location on your machine rather than the existing installation location, then install the license file by choosing the option Import a license from a File within the License Manager. This is described in our manual here:
To locate an existing license file from a Workbench installed to a different area of the machine, look in the folder called licenses for that other installed Workbench copy.
The License Manager of the Workbench should start up automatically when you start up the Workbench. If it does not, then you can launch it yourself by choosing the menu option:
Help | License Manager
- Launch the plugin manager and install any plugins you downloaded earlier by clicking on the Install from File button. This is described in our manual here:
You can now close the Workbench and then start it up again as a standard user. The Workbench is now ready to use.
1.9. How can I uninstall a CLC Workbench?
This FAQ page addresses how to properly remove CLC software from your machine. There are three elements that can be removed to fully uninstall CLC software. These include the application itself (including application binaries), supporting data such as preferences, and the data analyzed within the Workbench.
Information about how to remove each of these elements are provided here:
The CLC Genomics Workbench is used as an example in the following instructions. Other CLC Workbench software will have different names but the same steps can be applied.
Remove the Workbench Application
If you plan to install the Workbench software on the same system in the future and would like to keep software settings such as proxy server connection settings, license server settings, etc. the instructions in this section are all that you would need to complete.
For all systems, if you chose to create a desktop link or a symlink during the installation process, those shortcuts will also be removed.
- Please locate the uninstaller in the Workbench installation directory. The installation directory will be the location you chose to install the Workbench, you can also find where this is through the Workbench interface described in the FAQ: Where is my Workbench installation directory?
- Use the included uninstaller command to remove the Workbench software, this will be different for each operating system:
- Windows: Right click uninstall.exe and choose "Run as Administrator". This will remove the software and will deregister the software from the system registry.
- Linux: In the terminal run the uninstall command with sudo privilege or as root. For example
would uninstall the Workbench when the installation directory is /opt/CLCGenomicsWorkbench8/
- Mac OS X: Log into your Mac machine as the user who originally installed the Workbench. Through the Finder, double click the uninstaller application. For example, double click the CLC Genomics Workbench Uninstaller
- Windows: Right click uninstall.exe and choose "Run as Administrator". This will remove the software and will deregister the software from the system registry.
Remove Workbench settings and application data
Remove global application settings
You can remove the whole Workbench installation folder from your hard drive. This will remove the software files along with the license files and the global preferences settings for the Workbench. After the folder is removed, check that symlinks or shortcuts (e.g. desktop icons for the Workbench) are also removed. For example, on linux systems, there may be a symlink to start the Workbench in /usr/local/bin/
Remove all global application settings and the Workbench software by:
- Locate the installation directory of the Workbench. You can find where this is through the Workbench interface described in the FAQ: Where is my Workbench installation directory?
- Delete this directory using system tools. For example, you could use the
rm -rcommand on a linux terminal or delete this directory through the Explorer in Windows.
Remove user specific application settings
After the first run of the Workbench the user specific settings will be created under the user's home or profile folder. If you would like to remove them from your system, please refer to the following deployment manual page to find the locations of those settings folders and files based on the type of operating system you have:
Once you have located the "CLC bio" folder (or .clcbio on linux systems), remove it from the hard disk using system tools.
If there are multiple user accounts on the same system and they all have run the Workbench software at least once, then there will be multiple "CLC bio" folder (one in each user profile location) to be removed.
If you are planning to migrate the user settings to a different system, so that the same settings can be used for a new account on a different system, please make sure that the ownership and the filesystem permissions on these folders and files are properly set. This will ensure that the Workbench run by the new user account has the required read and write access within this CLC bio settings folder.
Remove the CLC analysis data
The CLC data is stored in one or more folders on the hard drive that you see in the Navigation Area in the Workbench. Uninstalling or removing the Workbench software will not affect the CLC data, unless in rare cases a customized data location was pointed to a folder under the Workbench software installation location.
If you wish to remove the CLC data, or move the CLC data folder(s) to somewhere else (e.g. a bigger hard drive), please refer to the FAQ articles for detailed instructions: How can I move my CLC data?
1.10. How do I download the software if I get a message about the signature being corrupt or invalid?
The CLC software installers are signed with a valid signature.
It should be possible to open the properties of the installer on your new computer and check. How to do this on a Windows 7 system is shown below.
November 2013: A recent Microsoft security update causes IE to (wrongly) report that the signature on our installers is corrupt or invalid. This issue exists for other software as well as CLC software. If you are encountering this issue and cannot download the installer file for CLC software, please try using another web browser. You can then check the signature on the downloaded installer, should you wish.
1.11. What does "error code 34" mean when I run the installer?
When working on a Windows system where the download of the installer file did not complete successfully, you will see "error code 34" message when you run the installer. An image of this is shown below.
To resolve this issue, please download a new installer file and try the installation again.
If your web browser offers the options of either running or saving the file please select the save option, then run the installation once the download has finished.
Information about where to get installer files is provided in a related FAQ entry: Where can I get installer files for the software?
1.12. How can I get a copy of the SDK?
CLC bio provides software developer kits, SDKs, for our Workbenches so you can develop your own plugins for the software.
If you plan to develop plugins that will make use of tools only available in the CLC Genomics Workbench, then you will need both the standard CLC Developer Kit as well as the Genomics Developer Kit. The latter requires a special license. Please see the related FAQ entry on how to get a license for this. You will also need a licensed version of the CLC Genomics Workbench.
For developing plugins using functionality of the Main Workbench, you need just the standard CLC Developer Kit . No license for this SDK is needed, but you will need a licensed version of the Main Workbench.
To get the SDKs, please register for an account out the CLC Developer Connection site:
Once you have an account, you can find documentation as well as the developer kit software itself here:
1.13. What does it mean if a Mac installer says it "is damaged and can't be opened"?
If you are working on Mac OS X 10.9.2 or newer, you may see a message about a software installer being damaged when you try to launch it. e.g. saying the software "is damaged and can't be opened. You should eject the disk image" or that the software "is damaged and can't be opened. You should move it to the Trash."
Newer Mac systems include a security setting that can block the installation of apps downloaded from places other than the Mac App Store. To install QIAGEN software, you need to allow apps downloaded from identified developers as well the Mac App Store. Do this by adjusting your security settings:
- Go to System Preferences | Security & Privacy
- Click on the padlock icon at the lower-left corner to enable you to make changes.
- Choose "App Store and identified developers"
We sign our software with a Developer ID from Apple. With the above setting chosen, you should be able to install our software. You will see a message warning you that the software has been downloaded from the internet, and asking if you wish to open it. This is expected, and you can proceed with installing the software.
Security settings affect your whole system. If you generally do not want to allow apps downloaded from anywhere except the App Store, then change the security settings back to the desired setting after you have finished installing your QIAGEN software.
If you continue to see this issue with the "Allow apps downloaded from" option set to "App Store and identified developers", please report this problem by emailing AdvancedGenomicsSupport@qiagen.com Please include the full name of the installer, when you downloaded it and the URL of the page you visited to download it from.
If you wish to proceed with installation anyway
If you are certain you obtained the installer via official channels and thus wish to proceed with installation anyway, information on how to do so is below.
Mac OS X 10.9.2 to 10.11.x
In Mac OS X 10.9.2 and newer, there is a security setting that must be changed so that the downloaded installer can be opened. To change this setting on Mac 10.9.2 through 10.11.x, please take the following steps:
- Go to System Preferences | Security & Privacy
- Click on the padlock icon at the lower-left corner to to enable you to make changes.
- Select the option for Allow apps downloaded from: to Anywhere
- Close the security settings window
- Double click on the installer file again and click the Open button when prompted.
We recommend reverting your security settings after installation of the software is complete.
Mac OS Sierra 10.12.x
The premise is the same as shown for Mac OS 10.9.2 through 10.11.x except that the steps to enable the "Anywhere" option are different.
If you view your security settings under System Preferences | Security & Privacy, you will see there is no Anywhere option.
To enable the "Anywhere" option, run the following command in a terminal:
sudo spctl --master-disable
If you go back to System Preferences | Security & Privacy, you will see the Anywhere option enabled. Unlock the edit option by clicking on the padlock icon at the bottom of the window to change to Anywhere option.
At this point, you should be able to install the software.
This security setting affects your whole system. To reinstate the earlier security policy, run the following after the software is installed:
sudo spctl --master-enable
and then check your security settings are as you expect.
2. Data and files
2.1. Where are the Workbench logfiles?
The logfiles* created by the CLC Workbenches are called
The location of these files is specific to the OS being used:
User home -> .clcbio -> workbench -> log
Windows 7, Windows 8 and Windows 10:
C:\ -> Users -> %username% -> AppData -> Roaming -> CLC bio -> Workbench -> log
/Users/%username%/Library/Application Support/CLC bio/Workbench/log
The Library folder is hidden by default. You can view it by opening a Finder window, pulling down the "Go" menu and then holding down the shift key. The Library option should then be visible in the menu. Click on it and then navigate to the location above. Alternatively, choose the Go to Folder option under the Go menu and then enter the path above into the text box, replacing %username% with your username, and click Go.
Locations on older systems (no longer supported) that are different from above
Mac OS X 10.6 (Snow Leopard)
User home -> Library -> Application Support -> CLC bio -> Workbench -> log
On Windows 2000 and XP
C:\ -> Documents and Settings -> %username% -> Application Data -> CLC bio -> Workbench -> log
* On CLC Main Workbench 6.7 and earlier and CLC Genomics Workbench version 5.5.2 and earlier, there are only two log files: output.log and error.log.
2.2. Where is my user settings file?
The user settings for your CLC Workbench is called usersettings.xml It is found in different places on different operating systems. Please replace the text within the %percent signs% to the appropriate text for your machine and Workbench.
$HOME ->.clcbio -> workbench -> settings -> %workbench name% -> %version number%
/Users/%username%/Library/Application Support/CLC bio/Workbench/settings/%workbench name%/%version number%/
The Library folder is hidden by default. You can view it by opening a Finder window, pulling down the "Go" menu and then holding down the shift key. The Library option should then be visible in the menu. Click on it and then navigate to the location above. Alternatively, choose the Go to Folder option under the Go menu and then enter the path above into the text box and click Go.
Windows 7, Windows 8 and Windows 10
C:\ -> Users -> %username% -> AppData -> Roaming -> CLC bio -> Workbench -> Settings -> %workbench name% -> %version number%
Newer versions of the Windows operating system may hide this directory location. If you are unable to see this location then please follow the instructions provided by Microsoft to show hidden files:
Locations on older systems (no longer supported) that are different from above
On old Mac versions:
Macintosh HD -> Users -> %username% -> Application Support -> CLC bio -> Workbench -> settings -> %workbench name% -> %version number%
Windows 2000 and XP:
C:\ -> Documents and Settings -> %username% -> Application Data -> CLC bio -> Workbench -> Settings -> %workbench name% -> %version number%
2.3. Where is my CLC Workbench data?
The following information is pertinent to both backing up data or if you plan to move your Workbench from one machine to another and wish to transfer the data.
There are two main sources of data available via a CLC Workbench:
In addition to backing up your data, you may also wish to save your usersettings.xml file. The location of that file on different operating systems is in a related FAQ question, linked on this page.
The data you import or generate using your CLC Workbench, which you can see listed in the Navigation area of the Workbench, is stored in data locations.
The easiest way for most people to find out where their data is stored is to put the mouse cursor over the top level directories in the navigation area of your Workbench. This brings up a tool tip, which tells you the system location for that data location.
To back up all your CLC data, you need to ensure that all the these system locations, that are set as data locations for your CLC Workbench, are backed up.
Information about your data locations is stored in an xml file called
model_settings_300.xml This file is located in the
settings folder in the user home. Further details about this file and how it pertains to data locations in the Workbench can be found in our Workbench deployment manual:
It would generally be unusual to choose to back up BLAST databases, as it is usually straightforward to re-download or re-create BLAST databases. However, if you wish to back up your BLAST databases, please refer to our manual for how to find out what directories you are storing these in:
Then just ensure these directories are configured to be backed up.
2.4. How can I add a new data location to the Navigation Area?
After installation, there will be a single data location in the Navigation Area called CLC_Data.
Information about where that folder is on the system and how to add other data locations in your Workbench can be found in the manual here:
2.5. How can I set a different default location for data to be saved into?
The default data directory can be changed for the CLC Workbenches at an individual user level, or for all users of a particular installed copy of the Workbench.
Changing the default directory for an individual Workbench user
The default data location for CLC Workbenches is, by default, a folder called CLC_Data in a user's home area.
This can be changed to a different location for a particular user of the Workbench by going to
Edit | Preferences
and then choosing the Advanced tab. There is a section there called Default Data Location and you can choose a default from a drop down list of data locations you have already added.
How to add a data location in your Workbench is covered in the manual here:
Changing the default directory for all users of a particular Workbench installation
There is an alternative method that is useful if there are multiple users of a single Workbench installation. The method to change the default location for all users of a particular Workbench is covered in section 8.2.2 of our Workbench Deployment Manual:
A direct link to that section of the manual is here:
Please note that if the CLC Workbench has previously been run, you will need to remove the file that is storing the current data location settings, model_settings_300.xml. The removal of the model_settings_300.xml file will need to be done for each user that has been using the Workbench. That file can be found under the folder called settings that is found under user-specific paths, described here:
After the model_settings_300.xml is removed, and the path.properties file is created, with a datadir line, as described in the Workbench Deployment Manual, then all users of your Workbench will have the specified directory as their default data area.
2.6. How can I move my CLC data?
New hard drives, machines, or server storage space may result in the need to move your CLC data: the data used as input for analysis tasks as well as the results generated. This FAQ article provides instructions to move your CLC data files to a different location.
Move your CLC data to a new storage location
The following are instructions for moving your CLC Data to a new location.
- Locate the CLC Data you wish to move on your hard disk. Please see the FAQ: Where is my CLC Workbench data? for instructions on how to do this.
- Create a new directory with a unique name in the location you wish for your data to be stored. For example, if you are copying the default CLC_Data folder to D:\, name this new directory to something like D:\CLC_Data_D, or another name that does not already exist as a Data Location in the Navigation Area of the Workbench. Please create this directory using system tools such as Window's Explorer, Mac's Finder, or any other file browser available on your system.
- Copy the data from the location it is stored (step 1) to the new desired location (step 2). You may do this via the command line using tools such as
rsyncor any other system tool you are comfortable using like the graphical interfaces suggested in step 2.
- Add the new Data Location to the Navigation Area of the Workbench:
- Open the Workbench
- Go to the top Toolbar | New | Location | New File Location
- Choose the folder that you have copied the data to (step 2 and 3)
- Reindex the new Data Location
- In the Navigation Area, right-click on the folder for the newly added Data Location.
- Click the Location | Rebuild Index option from the pop-up menu. Please do not run any jobs within the Workbench after beginning the reindexing process.
- Restart the Workbench after the indexing task has completed.
- Check the data in the new location is all present and can be opened successfully in the Workbench. This is to ensure the data copied successfully and was not corrupted in the copy process. If data is missing or corrupt please re-copy this data.
- Remove the old Data Location from the Workbench
- Delete the data (located in step 1) from disk using system tools.
Please be aware that the CLC Data location folders are meant for hosting the CLC (.CLC) data, not raw data. The raw data, such as the raw sequencing reads (.fastq, .sff, etc.) or the exported data from the Workbench (.BAM, .fasta, etc) should be stored in a separate folder or directory that is outside of the CLC data location.
BLAST databases can be moved similarly to what is described above. The only difference is that the BLAST database location is specified by using the Manage BLAST Databases tool:
- Create a new directory and copy the desired BLAST database data to this new location
- Add the new BLAST database location(s) with the Manage BLAST Databases tool
- Remove the old copy of the BLAST database folder via the Manage BLAST Databases tool
- Delete the old BLAST databases from the old location on the hard drive
Please also check the FAQ pages in this Data and Files chapter for related topics.
Data access permissions
If you are moving your CLC Data such that it can be used on a different system or instance of the Workbench, please make sure the system user account used to run the Workbench software has complete access to all data files. This includes hidden metadata files (index files) in the Data Location added.
If the CLC Data will be accessed by different users where different system user accounts are running the Workbench, please set folder permissions on the new CLC Data Location directory with recursive or inheritance settings such that all expected users will have read and write access to the data. Please adjust these settings on the parent folder instead of individual files to ensure all the contents of the CLC Data Location folder are accessible by all user accounts. You may need to contact your organization's IT support staff to assist you with this.
CLC data, that which is analyzed in the Workbench, is stored in a different location from the application binaries and user setting files by default. This means that, with default settings, if you uninstall the software, the CLC data will remain on your hard drive. It also means that in order to backup the CLC data, you will need to include the CLC Data Locations. The location of the CLC data is described in the FAQ: Where is my CLC Workbench data?
More information about the locations of CLC related files is described in the Deployment Manual: Where do we put things
2.7. Where are my temporary files to be written to and how can I change this?
The default location that temporary files are written to by CLC software is the system temporary file area.
For CLC Workbenches
Information about where the temporary files are being directed to can be found directly in CLC Workbenches from version 7.0 onwards by bringing up the "About" information for the Workbench from under the Help menu. For example, for the Genomics Workbench, use the menu option:
Help | About CLC Genomics Workbench
Then go to the File Locations tab.
You can find information on how to re-direct where temporary files are written to by the CLC Workbench in our deployment manual:
For CLC Servers
If you are not sure where the temporary files are being written to, you can look inside the output.log file, which you cand find in the installation area of the Server software. Just look for the line that starts with:
You can find information on how to re-direct where temporary files are written to by the CLC Server software in the Server manual:
For the CLC Assembly Cell
Temporary files are written to the directory specified in the TMP variable on Windows and TMPDIR on Linux and Mac. Redirection of temporary files involves setting these variables to point at the desired location.
In all cases
We highly recommend that temporary file space be set to areas on the local file system. Having your temporary file space on a remote filesystem can cause the performance of the software to be significantly reduced.
2.8. Where is my Workbench installation directory?
The disk location, or installation directory, the Workbench is installed in can be found through the Workbench software:
- Go to Help | About CLC ... Workbench
The "CLC ... Workbench" text that you see will differ based on the particular Workbench you are working with; eg. the CLC Genomics Workbench will show the text "About CLC Genomics Workbench" from this help drop down menu.
- Click on the File locations tab.
- The installation location information is listed under the Application directory as shown in the screenshot below.
2.9. Why is my data location greyed out in the Workbench navigation area?
If you have configured a CLC data location and it appears greyed out in the Navigation area, it suggests that the underlying data area is not available to the user that is running the CLC Workbench process. Common causes and solutions are:
Problem 1: The underlying folder on her system that you have configured as a CLC data location has been moved or removed, or your Workbench was started up before a drive with the CLC data location was mounted.
Solution to problem 1: If you hover the mouse cursor over the folder configured as the CLC data location, you should see the full path to the data location you have configured. Please check that the location exists on your system and that you have access to it.
Once the location is available on your system, try updating the data locations. This can be done by clicking on the update all button, show in the figure below.
If the data area is not local to your machine and you need to provide log-in credentials to get access to it, then you can use normal system tools, such as a file browser window, to access it, and then enter your user credentials when prompted. After this, if the CLC data area in the Workbench is initially greyed out, click on the update all button as suggested above.
If you still have problems after taking the above steps, then please restart your Workbench and see if this resolves the issue.
Problem 2: You are running the CLC Workbench as a user that does not have permission to view the folder you have configured as a CLC data area.
Solution to problem 2: Check whether the user that you are running the CLC Genomics Workbench as has permissions to view the folder you are trying to access. If you wish to save data to that area, you will also need to have write permissions for that area.
** Note: ** If you have just upgraded your Workbench, and chose to restart the Workbench when prompted during the installation prociess, then it will be running as an administrative user. In this case, please try closing the Workbench and starting it again normally.
If the above problem descriptions or solutions help, please send an email to AdvancedGenomicsSupport@qiagen.com
2.10. Why are temporary files still written to the old default location after I redirect them?
One can specify a new location for temporary files created by the CLC Workbench (see related page linked at the end of this page). If you have tried to do this, but the files are still being put into your system's default temp location, this is usually easily fixed and is usually due to one of the issues listed below.
- Incorrect formatting of the file location within the path.properties file, OR
- Incorrect naming of the path.properties file
- Incorrect content in the path.properties file
- path.properties file is saved to the wrong place
The most common issues here are
- typos in the path provided
- incorrect characters used in the path
One common slip is the direction of the slashes used in file paths on Windows systems, where backslashes (\) are used, and those used on Linux and Mac systems, where forward slashes (/) are used.
For example, the following is an acceptable style of writing a path on a Linux system:
whereas the following is an acceptable path on a Windows system:
The name of this file must be exactly and only
There is a particular problem with some Windows programs where text files are automatically given a suffix .txt when you create the file. This can be hard to spot if the option to hide file extensions is enabled. Microsoft provides some information on how to disable this option here:
Please change the file name so that it is exactly and only
The file path specified must be suitable for your operating system and you must spell tmpdir as tmpdir. An example path.properties file, with some additional information in it, can be found here:
As an example, on Windows, the following would re-direct temporary files to the D: drive , to a folder at the root level on that drive called CLCTemp:
tmpdir = D:\CLCTemp
The following versions would not work:
tempdir = D:\CLCTemp
Tempdir = D:\CLCTemp
tmpdir = D/CLCTemp
The path.properties file must be saved in the folder called settings within the installation area of the CLC Workbench that you plan to run. Issues that can arise associated with this include:
- The path.properties file was saved to a settings folder in a different copy of the CLC Workbench then the one you are running.
If you are starting up the Workbench by double clicking on an icon, please check where the actual program being launched is located, and then ensure that you are placing the path.properties file in a folder called settings within the installation area of that particular copy of the Workbench.
- The path.properties file was saved to a folder of a different name.
If you have problems and none of the other solutions on this page explain it, please double check that the path.properties file was saved into a folder called settings within the installation area of the Workbench you are running.
If you have worked through all the above and there are still problems getting your temporary files to be written by the Workbench to your new location, then please contact Support as described in the linked page at the bottom of this page. Please include in your description the line you have used in your path.properties file to define the new temporary directory location.
2.11. What does an error about problems writing to temp mean?
During analyses, CLC software often writes data into an area designated for temporary files. This is sometimes referred to as a "temp" or "tmp" area. The most common issue when writing temporary files to the designated area is that there is not enough space available. When this occurs, errors about problems writing to temp (or tmp) are reported.
To solve the issue, you need to either clear space in the relevant area or re-direct the temp directory to somewhere with more free space. (Please see the related FAQ entry for how to do this.)
Very occassionally, errors writing files to temp may arise when you do not have permission to write to the designated area. This is unlikely to happen in the case of a default installation, but could happen if someone has re-directed where software should write temporary files to and has set a location you do not have permission to write to.
In practice, permissions issues in this context arise only very rarely. Running out of temp space is, by contrast, relatively common, especially when one first starts working with the large NGS datasets and is still determining an appropriate configuration for the local requirements.
2.12. How can I delete a whole data location and all its contents?
For CLC Genomics / Main Workbenches and Biomedical Genomics Workbenches:
Before removing the data files and the data location(s) hosted by the CLC Workbench software, please make sure that the data have been properly backed up and stored to avoid data loss due to accidents.
While the CLC Workbench software is closed, copy the data folder over to the new storage area to be used with filesystem tools such as copy and paste. Once the data files are in place, please start the CLC Workbench, then add the new CLC data location based on the instructions at
and then point this data location path to the data folder that was just copied over.
You can then set the default CLC Data location to the new location within the Workbench. More information about setting the default data location is available at
Once the default data location has been assigned to the new partition, you can simply remove the old data location by right clicking on the location folder in the navigation area and choose Location | Remove Location.
Before you delete the original CLC Data folder from the filesystem, please do the following to verify that the data in the new location are working as expected:
a. rebuild the data index
- Go to the topmost folder in the location tree on the left hand side of the Workbench, under which the object in the error report is stored.
- Right-click on this folder.
- In the menu that appears, choose Location.
- Choose to Rebuild index.
- Once the process is completed, restart the Workbench software.
b. run a couple of analysis with the data from the new location as input, and then save the data into the new data location to verify that the software have both read and write access to the data folders on the new partition. For example, run the Create Sequencing QC Report tool on the imported read data and save the report into the new location
2. Remove the temporary folder to the new partition
You can find out which location your Workbench is writing temporary files to by going to
Help | About CLC Genomics Workbench
and then clicking on the "File locations" tab.The default temporary data location may contain data required from other non-CLC applications. You can remove the CLC temporary data by deleting the sub-folders with names starting with "CLC-" while the Workbench is closed.
For CLC Genomics Servers:
Before removing the data files and the data location(s) hosted by the CLC Server software, please make sure the data have been properly backed up and stored if they are needed in the future.
You will need to be able to log into the Genomics Server web-based thinclient with privileged account (e.g. root) on the CLC Server to do this.
After logging in as root, the data folder or directory path(s) can be found under Admin | Main configuration | File system locations
Please record the paths and then remove the locations by using the "Remove Location" button next to each data location path.
After the changes to the data locations have been saved, and that the CLC Server service is restarted, you can then proceed to remove the data folder or directory on the filesystem of the same paths previously configured on the Genomics Server.
More information on the data location of the CLC Server is available in the following manual link:
The temporary data location is either located on the system default (e.g. /tmp on linux) or in a customized path specified in the CLCGenomicServer.vmoptions file found under the software installation location. While the server service is closed, you can then remove the sub-folder within the temporary location with the name starting "CLC-".
If you wish to redirect the temporary folder for the single server or the job node setup, follow the instructions described in
For the Genomics Server running grid integration as the backend, please locate the grid worker temporary location by referring to the instructions in
3. System and resources
3.1. What is the difference between running a Genomics Server and running a Genomics Workbench on a large central machine that multiple users can access?
If you are working in a group with multiple users who wish to make use of the Genomics Workbench analysis tools on a central machine, it is possible for members of your group to
- share access to a single Genomics Workbench using a network license via remote desktop on the central machine, or
- connect to a Genomics Server running on the central machine from a local Genomics Workbench such as from the user's own laptop or a desktop computer.
such that multiple users can run analysis tasks on the large central machine. The primary differences between these two set ups are related to
- Job Queue
- Multiple Users
- Data Access and Permissions
The Genomics Server allows for a large number of jobs to be submitted to it such that each job submitted will be placed in a queue and executed when the available job slot is available. The Workbench, however, will not queue jobs, but will run them immediately, without regard for other concurrent processes or available resources. For example, if you have a network license for the Genomics Workbench, and five separate users choose to each runs a large de novo analysis on the central machine through remote desktop protocols such VNC or RDP. Each of those analyses thinks it has rights to the memory of the whole machine because the Genomics Workbench was designed to consider single user on a single machine. As a result, all jobs are launched as they are submitted. If simultaneously running analyses are large, it is very likely that the Genomics Workbench will crash with an out of memory error caused by resource competition.
Alternatively, if 5 de novo assembly jobs are submitted to the Genomics Server, they will be queued such that each will run one at a time or only one job will run per execution node. More information about the queue can be found
There are other benefits of the Genomics Server, especially if you are running a service. It is designed with the idea of multiple users, in a way that the Workbench is not. This includes the authentication system, the audit log, the ability to have installed Workflows that are available for all users, and the ability to control who has the rights to run certain tools or has the access to certain data folders. For example, maybe your service doesn't include de novo assembly. You can control access to allow the users to run all but the de novo assembly tools on the server.
Data Access and Permissions
The data access and permission configurations for the Genomics Server are described in
You can always configure the data file access and permissions (in .clc format) through filesystem or sharing security policy. They both overwrite the application level access control configurations. The application level configurations for data access can only be configured within the Genomics Server. The Workbenches, as described above, has single user design and does not have the in-program data file access and permission settings. If you have a centralized data sharing servers, then having the Genomics Server will be advantageous in terms of managing the CLC data through the application level settings.
There are also more general features available via a Genomics Server that are not available via the Workbench, such as the use of the Command Line Tools as a client (instead of the Genomics Workbench) or the ability to tie into other local tools or in-house pipelines using External Applications.
Of course, only you can decide what would suit you best, but unless you plan to offer your service to only a very small group of people who are in tight communication with each other (e.g. they will not all launch large jobs at the same time). Perhaps one way to consider this further is to work your way through the options in the administrative interface of the Genomics Server. Apart from the ability to set up File system locations (known as Data Locations in the Workbench), install Plugins, install Workflows and set up blast data locations, all the other functionalities referred to in that interface are only available on the Genomics Server. So this may help in your considerations.
3.2. Are the tools of the CLC Workbenches or Servers multi-threaded?
A list of analyses offered by the Genomics Workbench, Biomedical Genomics Workbench or the Genomics Server that benefit from the availability of multiple cores can be found on this page of our manual:
The tools listed are those that could benefit from running on computers with multiple CPU cores, but this does not mean that they use all CPU cores available the whole time.
For the CLC Main Workbench, the only analyses that make use of multiple cores are the 'Create Alignment' tool and 'BLAST'.
While Workbenches can be run on systems with just one core, your experience will generally be much better on a machine with at least 2 cores. This can make a difference for running analyses, but will also make a difference when it comes to viewing large or complex datasets, such as read mappings or alignments.
The following pages of our manual may also be of interest:
Restricting the number of cores that the Genomics Workbench analyses can use:
Restricting the number of cores that the Genomics Server can use:
Please note that some analyses include a native binary phase, and the binary phases of these tasks are not currently affected by such restrictions you put on the java process. Analyses with a native binary phase are:
- De novo assembly
- Read mapping
- Extract and counting tags for small RNA analysis and Expression Profiling by tags
- Blast searches*
*BLAST is an exception in that we use the NCBI binaries directly. Here, the maximum number of threads used by a local BLAST search is configurable via the Wizard for any given job.
3.3. How do I change the memory limit for the CLC Workbench or Server java process?
The default memory setting and how to change it
The amount of memory, which can be utilized by a CLC Workbench or CLC Server java process is initially set during the installation of the software. The default amount of memory set in the case of the Workbenches, or suggested in the case of the CLC Server, is the lesser of 50% of the available physical memory or 50GB. We generally recommend that the setting be left at the default level.
It is possible to alter it.
You will find information on how to change this setting in the CLC Workbenches in our deployment manual:
For how to change this setting for the CLC Genomics Server, please refer to the Server manual entry:
Why only 50%?
The default setting, specifying that the maximum amount of memory the Workbench java process should use reflects that fact that space should be available for other system operations and that certain Workbench tools have binary phases - that is, phases that do not run as part of the java process. Binary phases of such tools use memory outside that used by the Workbench process itself and are thus not subject to the memory settings in the vmoptions file. Tools with this profile include de novo assembly and analyses that include a read mapping phase (e.g. read mappings, RNA-seq analyses, small RNA analyses, etc.) and local BLAST searches.
Why only 50Gb?
The 50GB limit is to prevent pauses caused by the garbage collector (GC). In addition to ensuring free memory for the external binaries, as mentioned above, the recommended limits on maximum heap space are there to ensure that the JVM does not spend too much time running garbage collection (GC) processes. The GC is a memory handling subsystem of the JVM, which scans through the currently used heap, and frees up memory by removing contents no longer in use. The larger the maximum heap, the longer each check through the heap will take. The JVM has to suspend all other activities while running the GC - these suspensions are on the scale of milliseconds to a few seconds, and are normally not noticeable.
In combination with the GC subystem of the JVM, the CLC Workbenches and the CLC Genomics Server utilize a sophisticated caching system, moving unneeded data out of memory and in to temporary disk storage. The result of this caching system means that there will not be any noticeable performance improvement with a Java heap space larger than 50GB, while GC pauses may become more noticeable.
3.4. Can I limit the number of CPUs used by a CLC Workbench?
Restricting the number of cores that a CLC Workbench can use is covered in our Workbench Deployment manual here:
3.5. Why is the Workbench/Server holding onto memory between jobs?
The CLC Workbenches and Servers hold on to very little in-memory data when idle. The actual heap space memory consumption should be less than 100MBs of live data when idle. However, the Java process' memory allocation strategy is left completely up to the Java Virtual Machine (JVM).
The memory consumption seen when the Workbench or Server is not running analyses or other actions is allocated virtual memory address space (which the JVM by default releases only reluctantly, once allocated), not physical memory pages. Thus it should not be a problem that the java process holds onto this memory until it is required elsewhere.
Some further details about memory settings in Workbench and Server products
The normal installation script for the CLC software by default sets this memory allocation to the lower of either 50GB or 50% of the total available memory. These are the values we would generally recommend. The reasoning behind the 50% value is that memory-intensive tasks, for example, de novo assembly and read mappings, are carried out by external binaries that can end up in competition with the java process for the available memory, depending whether other Workbench or Server tasks are also demanding that memory and expecting it to be available.
How to change the Java process' memory allocation for Workbenches can be found in our deployment manual:
How to change the Java process' memory allocation for CLC Server products can be found in Server administration manuals:
3.6. Which internet addresses does CLC software need access to?
Some functionality available in CLC software requires access to specific addresses on the Internet. Below, we provide a list of addresses the CLC software tools will try to access and the names or descriptions of tools that use those sites. If the machines being used have direct access to the external network, then you should not need to do any further configuration to run the tools involved or download data, plugins, licenses and so on.
For machines not directly connected to the external network, the list of sites below can be referred to when configuring firewall settings for networks that utilize a whitelist approach. If you are using a CLC Server with a cluster or computing grid backend, the nodes in the cluster will also need access to the sites listed for particular functionality to work. For example, if you wish to run Ingenuity Variant Analysis on a CLC Server with nodes, the nodes that could run this tool must be able to contact *.ingenuity.com.
The majority of these addresses are provided and controlled by third parties, and specific addresses may change without prior warning or notice.
Some third party plugins may require access to additional addresses, which are not included in the list. Further details for such plugins should be requested from the plugin provider.
Enable FTP*, HTTP and HTTPS for all desired functions from the list below.
*FTP protocol requires the firewall to support REST, PASV, and RETR commands.
|Workbench update information,
plugins, download license
|Download BLAST databases||ftp.ncbi.nlm.nih.gov|
|Download Sequence Read Archive (SRA)||sra-download.ncbi.nlm.nih.gov (only http or fasp)|
|BLAST at NCBI||blast.ncbi.nlm.nih.gov|
Search for sequences at NCBI
Search for PDB 3D protein structures at NCBI
|Download Pfam database||ftp.ebi.ac.uk|
|Uniprot database search||
|Microbial Genomics Module
(OTU amplicon-based databases)
|Microbial Genomics Module
|Microbial Genomics Module
(Pathogen Reference databases)
|Microbial Genomics Module
|Microbial Genomics Module
(Gene Ontology databases)
Ingenuity Pathway Analysis
List updated March 6, 2019
3.7. Why does the Workbench 3D Viewer throw a OpenGL error suggeting that my graphics card needs updating?
With the release of CLC Genomics Workbench 6.5 and CLC Main Workbench 6.9 (and any future versions), a new 3D viewer was introduced. This uses an OpenGL Application Programming Interface and requires a graphics card with proper OpenGL 2.0 support. This means that users with old graphics cards or old graphics card driver, or if the Workbench software is running from a platform (e.g. older version of virtual machine with no 3D sopport) may encounter problems launching the software and will need to either upgrade the driver or switch to a more compliant platform in order to work properly.
The graphics requirements for CLC software are described in
Updating your graphics card drivers:
Note that on Windows the 'Windows Update' facility may state that your graphics card driver is up-to-date though this is not the case.
To update your drivers you may want to first check the web page of the relevant computer manufacturer. These often have a download section with e.g. driver updates.
It may be necessary to go to the manufacturer of the graphics card in order to get the most recent driver and hence solve the problem. You will be able to look up the graphics card details and name of the manufacturer on your machine.
A 64-bit workbench version is strongly recommended (because of the way we currently reserve Java memory for 3D rendering).
3.8. Will a high spec graphics card improve CLC Workbench performance?
The Genomics Workbench performance does not improve noticeably through use of special or high-performance graphics cards. CLC software is accelerated through the utilization of the SSE instruction set, via the CPU. GPU acceleration is not supported.
The only recommendation related to graphics card capabilities is for the card and associated drivers to support OpenGL 2.0, as described in the Genomics Workbench manual here:
OpenGL 2.0 is primarily used to support the 3D molecule viewer for viewing protein structures.
Some people find that increasing the available screen area, either using a larger display or multiple displays. can be beneficial when working with CLC Workbenches. Thus, if the physical environment surrounding the workstation allows for multiple displays, it may be of benefit to select a graphics card that supports multiple displays.
The current CLC Workbenches support multiple displays as described in the manual page linked below:
3.9. Can I run CLC Workbench software on a machine that is not network connected?
CLC Workbenches can be run on machines that do not have a network connection. Only the functionality that relies on contacting the external network would be affected. Such functionality includes:
- Downloading a license. This will have to be done on a different machine. Please see the related FAQ for information on this.
- Software updates. Installer files need to be downloaded to a networked machine and then copied across to the non-networked machine.
- Plugin downloads. To install plugins on a non-networked machine use the option "Install from File" in the Plugin manager to install plugins from cpa files. You can download these files for the latest release of the Workbench from the plugins webpage: https://www.qiagenbioinformatics.com/plugins/
using a networked machine and copy them across to the non-networked machine.
- Reporting errors cannot be done by clicking the button in an error window that invites you to submit the error. If you see an error window, please dismiss it, but then, before running other tasks please collect and send us the log files via email as described in the FAQ entry: Where are the Workbench logfiles?
- Using the Contact Support option will not be possible. Please just send us an email.
- Internet-related functions inside the Workbench such as "Search sequences (or structures) at NCBI or in UniProt", as well as "BLAST search at NCBI", "download BLAST databases" functionality will not be available without access to the external network.
4. Starting up and running the Workbench
4.1. Which tasks require me to run the Workbench as an administrative user and how?
To install or make changes to your license, modify proxy server connection settings, or install plugins, you must run the Workbench as an administrative user.
For all systems, you must have permission to run the software as an administrative user. If you do not have this level of access, you will need to ask someone who does to run the Workbench and make the changes for you.
For Windows 7, 8, 10 or Vista, please close the Workbench, and then right click on the icon for the Workbench and choose "Run as administrator".
There are various ways one can start up the software as an administrative user on Linux. One way that is supported on many systems is:
- open up a terminal window
- type the command to start up the Workbench. prefaced with the term "sudo".
For example, if you opted to include a softlink to /usr/local/bin when you installed the software or you have otherwise placed the CLC Genomics Workbench on your PATH, you should usually be able to type:
If the above does not work, try using the full path to the software. For example, if you were working with CLC Genomics Workbench 10, or any subversion of this (e.g. 10.0.2 or 10.5.1) and you chose the default installation, you could type the following to start up the Workbench as an administrative user:
Please have the user who originally installed the Workbench login and make the changes. If this user is not longer available you will need to change the ownership of the installation directory and files for your Workbench, effectively changing the administrative user on your Mac. First open the 'Terminal' application which you may find with Spotlight. Then enter the following command - please change the Application directory to the appropriate path if your Workbench is not installed in the default location:
sudo chown -R $USER "/Applications/CLC Genomics Workbench 10/"
You will need to enter your Mac login password to run this command. Then you may open the Workbench and you should have administrative access.
Please restart the Workbench as a normal user after you have installed your license or plugins.
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:
- Something associated with your user settings is the source of the problem.
- The default Data Location is a shortcut.
- Anti-virus software is scanning the software.
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.
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 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.
4.3. Why can't I see the Workbench even though it is running on my Windows system?
There is a problem that can occur with any program on Windows where the graphical window moves off the visible screen.
When this happens with the CLC Workbench, the symptoms are that you can see the program is running when you look in the process table or taskbar, but you cannot actually see the Workbench window.
- Use Alt+tab to switch to the Workbench window. On Windows 7 this should also show you a thumbnail image of the Workbench window.
Press Alt+Space, followed by "x". This will maximize the window and match it up with the corners of your monitor.
- Alternatively, use Alt+tab to switch to the Workbench as before. Then press Alt+Space but this time followed by "m". Press any of the arrow keys on your keyboard once, and then use the mouse to reposition the Workbench window.
The Alt+Space menu of the Workbench looks like:
The "x" and "m" shortcuts are for an English version of Windows. If your Windows is a different language then you may need to use other shortcut letters. Any program that stays on your monitor should list the same menu with Alt+Space.
4.4. Why do I see a JVM error when I start up the Workbench?
An error like the one below can be due to a number of causes.
The JVM could not be started. The maximum heap size (-Xmx) might be too large or an antivirus or firewall tool could block the execution.
The causes include:
1) You are working on a 64 bit system and have mistakenly downloaded the 32-bit version of the Workbench, whereas you used to be running the 64 bit version of the Workbench.
If this may have been what happened, please download the 64 bit installer and try installing again.
2) You are working on a 32 bit Windows XP system with more than 2Gb of RAM. Here, your memory settings may be too high.** To check this, please find the file in your CLC Workbench installation directory that ends in ".vmoptions". (If you cannot see such a file, please ensure you have set your folder options on Windwos to allow you to see hidden files.)
Please decrease your memory setting in the vmoptions file to 1000m, and restart your Workbench. That is, edit the line that starts with -Xmx such that it looks like this:
3) Anti-virus software may be interfering with start up. You can test this by briefly turning such software off and see if your CLC Workbench then starts up.
If you have checked all these possibilities and you continue to see the problem, please email firstname.lastname@example.org with a detailed explanation of what you are seeing. Including screenshots of the error can often be helpful to us in trying to troubleshoot the issue.
4.5. Why is the Workbench sometimes slow on OS X Mavericks and later versions?
A new feature introduced in OS X Mavericks, App Nap, can dynamically reduce the processing power available to individual applications.
This can result in slow processing of tasks by the CLC Workbench if the machine switches to screen saver or is otherwise left running unattended.
App Nap can be disabled per application.
To do so, please right-click the CLC Workbench app and select "Get Info".
Next, check the box labelled "Prevent App Nap".
The Workbench must be restarted for the change to take effect.
A screenshot below shows the above steps on how to disable the App Nap feature.
5.1. How can I install plugins in a CLC Workbench?
You can install plugins into your CLC Workbench using the Plugins manager. The Plugins manager is launched by clicking on the Plugins button in the top toolbar.
Please note that to install Plugins, you need to be running your Workbench as an administrative user.
Further details about handling plugins in the CLC Workbenches can be found in our user manual:
5.2. How can I install plugins in a CLC Server?
Details about updating server plugins can be found in the manual at:
A list of the available plugins for the CLC Genomics Server can be found in the Server plugins section of:
If the plugin you are looking for is not listed, it may be because not all Workbench plugins are available as Server plugins or because functionality, originally delivered in plugins, has been integrated into newer versions of the software.
If you have old versions of any plugins already installed in your CLC Genomics Server, please remove these and then update the plugin. All removal and installation of server plugins is done via the web administrative interface.
5.3. What do I do if I end up with .zip files instead of .cpa files when I download plugins from the website?
Plugins downloaded from the CLC bio website have the file extension .cpa .
When working on a Windows system and using Internet Explorer, you may find that when you download plugin files they have the file extension .zip .
If this happens, the simplest solution is to use a different browser software, for example, Firefox or Chrome, to download the plugins.
For any Workbench running on a machine connected to the internet, we generally recommend using the Plugin manager within the Workbench for downloading and installing plugins.
5.4. Why are no plugins listed in Download Plugins tab of the Plugins Manager?
The Plugins manager of the CLC Workbenches connects to our servers over the network to retrieve the list of plugins that are available to download and install.
If your Workbench is not able to connect to the external network, then you will see something like the image below when you open the Download Plugins tab of the Plugins Manager.
Another possibility that nothing is showing up in the available Download Plugins list is that all plugins have been downloaded previously. You should be able to find them under the Manage Plugins tab. Or you are running a beta Workbench software which does not (yet) support any plugins.
The most common cause of the network connectivity issue is where there is a proxy in place and the Workbench has not been configured to use it. Instructions for how to configure the Workbench with proxy information can be found in our manual at:
You can also configure the proxy settings directly by clicking on the button in the Plugins Manager labeled "Proxy Settings".
You may need to talk to a local IT person to find what the correct settings are for your site.
Once the proxy settings are configured, restart your Workbench.
If connecting to the external network is not possible on the machine the Workbench is installed on, then you can:
- Get the plugin files from our website using a machine that does have access to the external network.
- Copy those files onto the machine the Workbench is running on.
- Run the Workbench as an administrative user and then launch the Plugins manager by clicking on the Plugins button in the toolbar.
- Click on the "Install from File" button in the Plugins manager and select a plugin cpa file.
6.1. Where can I find the manual?
HTML and PDF versions of the manuals for the latest releases of CLC software can be found on our website:
For CLC Workbenches, the manual information is also available from within the software itself. This information can be accessed while working online or offline, and when you access the manual this way, the information will be relevant for the version of the Workbench you are running.
You can access the manual via the Workbench in two ways:
1) Go to the menu option
Help | Help
2) Click on the button label Help in the bottom left hand corner of Wizard windows when you are starting up a job. The Help button is also available in bottom right hand side of the Viewing settings pane when viewing data in the Workbench.