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CLC FAQ - General questions and contact information

1. Questions, errors and feature requests

1.1. Am I eligible for support for my CLC software?

Anyone running software that is using a license covered by the CLC Maintenance, Updates and Support program is eligible to receive support from us.

If you are contacting us by email, it can help if you include information about the license you are using. Further details on this can be found via the Related pages link on this page.

 

If the license you are using is not covered  and you would like to look into re-entering the maintenance, update and support program, please contact bioinformaticssales@qiagen.com about this.

If the license you are using is not covered  and you are not interested in re-entering the maintenance, update and support program, then we hope you will be able to find the answers to your questions among the manualstutorials and other entries in our FAQ area.

If you are working using an evaluation license, then you are eligible for support. In this case, please confirm that you are an running the software as an evaluation user by following the instructions in the Related pages link to send information about your license along with your questions or issue report.

If you are working without a license, using Viewing Mode, you are not eligible to receive support via our Support team, but are of course welcome to make use of any of our online documentation sources, including the manualstutorials and other entries in our FAQ area.

1.2. How do I contact the CLC specialist on the QIAGEN Bioinformatics Support team?

You can contact our Support team:

From within a CLC Workbench
Sending us an email
From the web admin interface for a CLC Server

Please also refer to our related FAQ entry describing eligibility for Support.


Via a CLC Workbench

If you have a question and are using the Workbench, then the best way to contact us is to use the tool in the Workbench under the Help menu at:

Help | Contact Support

Please include your full and correct email address in the form provided.

If you are reporting an error, please refer to our related FAQ: How do I submit an error report for a CLC Workbench to the CLC Support team?

To report problems using the Assembly Cell software, please use the support option described below.

 

Email

You can email us at ts-bioinformatics "at" qiagen.com.

If contacting us by email, it will help if you include information about the license you are using. Further details on this can be found via the Related pages link on this page.

 

From the web admin interface for a CLC Server

To submit your CLC Server logs, please go to the web administrative interface for the Genomics Server, and click on the "report a bug" link in the top right hand side.

If you are already in touch with us related to the issue you are sending a report about, please include the ticket number in the email line of your submission, for example: joeblogs@madeupplace.com 12300

On a machine with a network connection, you do the above and then just click on the button labelled "Submit Bug Report".

On a machine without a network connection, click on the button labelled "Download Bug Report", copy the zip file to a machine with a network connection and attach the log files in an email to us. Email contact is described in the section above.

Using this method results in the submission of a zip archive of your Server log files along with your request. If you have problems sending your report to us due to the size of the log file archive, then please use email to contact us, as described above, and let us know this. We will then create an ftp area that you can transfer the files to.

This method is generally intended for asking questions or reporting problems related to a CLC Server setup. For Workbench or Assembly Cell questions, please consider using one of the methods described above.



1.3. How do I submit an error report for a CLC Workbench to the Support team?

In many cases, an error report via the Workbench will supply necessary information for troubleshooting.


If you are running an analysis on a networked machine and an error window appears

Please click the button labeled "Submit error" to send the error report to us.

This is the best way to report an error to us, as reports sent this way will include much information that can help us troubleshoot the issue. If you are logged into a CLC Server at the time you submit a report this way, your CLC Server logs will usually be included in your error report.

You will usually get the chance to submit extra files when you send an error report this way. If small datasets are involved, this can be useful for troubleshooting. If large datasets are involved and we need to see those to get to the heart of the problem, then we will discuss this with you and arrange for another way to transfer the data.

If you are already in discussion with support about the particular issue you are reporting, please include the issue number in the subject lines of emails you have received on this topic.  For example, if 11011  was in the subject line of emails you have received from support, please ensure the Subject line in your submission includes the number:

11011

This will connect your report to the discussion thread already existing at our end.

 

    If you notice an issue with your CLC Workbench, but this does not result in an error window appearing
or
    If you are running an analysis on a non-networked machine and an error window appears,

You will not be able to just click a button to submit an error report to us. In this case:

  • If you are on a networked machine and the Workbench is running, then please choose the option to "Contact Support" under the Help menu of the Workbench, OR

  • If you are on a non-networked machine and/or the Workbench is no longer running, then please email ts-bioinformatics@qiagen.com and attach the logfiles for the Workbench to your email.  These are the files called output.log, error.log and clc-workbench.log.

    Please do not re-start your Workbench before taking a copy of the log files, as the output.log and error.log files are over-written each time the Workbench starts up.

    See the accompanying FAQ question for where you can find the log files mentioned above on your system.

    If windows appear with error messages in them, but no button inviting you to submit the error to us, then screenshots of these error windows may be useful.

If you are already in discussion with support about the particular issue you are reporting, please include the issue number in the subject lines of emails you have received on this topic.  For example, if 11011  was in the subject line of emails you have received from support, please ensure the Subject line in your submission includes the number:

11011

This will connect your report to the discussion thread already existing at our end.

1.4. How do I submit an error report for a CLC Genomics Server to the CLC Support team?

If the Genomics Server administrative web interface is accessible

To submit your CLC Server logs, please go to the administrative web interface for the Genomics Server, and click on the "report a bug" link in the top right hand side.

 

 

On a machine with a network connection 

If you are already in touch with us related to the issue you are sending a report about, please include the support request number in the email line of your submission, for example when the case number is 12300:

joeblogs@madeupplace.com 12300

Click on the button labelled "Submit Bug Report".

Please include a detailed a description of your question, or the problem you are experiencing.

 

On a machine without a network connection

  • Click on the button labelled "Download Bug Report"

  • Copy the downloaded zip file to a machine with a network connection

  • Attach the zip file to an email sent to ts-bioinformatics@qiagen.com, or the existing email message from the support team.

Using this method results in the submission of a zip archive of your Server log files along with your request. If you have problems sending your report to us due to the size of the log file archive, then please send an email to ts-bioinformatics@qiagen.com to let us know this. We will then provide alternative platform that you can transfer the files to.

 

If the Genomics Server administrative web interface is NOT accessible

Please create a zip (or compressed) file containing the following files from the Genomics Server installation directory:

  • output.log
  • logs/*
  • webapps/CLCServer/WEB-INF/*

Please email this compressed file to ts-bioinformatics@qiagen.com.

1.5. How do I submit an error report for a CLC License Server to the CLC Support team?

If you are having trouble with the CLC License Server, which is the software that is used to server CLC network licenses, then please:

  • send an email to ts-bioinformatics@qiagen.com
  • describe the issue you are seeing as completely as possible
  • attach the logfile for the CLC License Server to your email. This file is called licenseserver.log and can be found in the installation area of your CLC License Server software.

1.6. How can I find out more about my licenses?

Please see the question is the CLC Licenses FAQ area.

2. General questions

2.1. How can a reviewer or colleague view my results if they don't have a license for the software?

A CLC Workbench can be run without a valid license in "Viewing Mode". In this mode, import, export and viewing functionality is available. Please refer to the manual for further information about this mode.

CLC Genomics Workbench 
http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Viewing_mode.html

CLC Main Workbench
http://resources.qiagenbioinformatics.com/manuals/clcmainworkbench/current/index.php?manual=Viewing_mode.html

If data was generated using tools provided by a plugin or module, then that plugin or module may need to be installed to view the data. This can be done while working in Viewing Mode also.

 

If a reviewer wishes to do more than just view the data in a CLC Workbench, then evaluation licenses are available.  Check out the related FAQ area for information on evaluation versions of the software: Evaluation of CLC software

2.2. Where can I find manuals and tutorials?

Manuals for CLC software can be found at:

https://www.qiagenbioinformatics.com/support/manuals/#manuals

The manual s provide in depth information about CLC software.

 

Tutorials for CLC software can be found at:

https://www.qiagenbioinformatics.com/support/tutorials

This is the best place to get started with CLC software.

 

3. Evaluation of CLC software

3.1. How can I evaluate the software and how long is the evaluation period?

CLC Workbenches and the CLC Assembly Cell

If you have not previously evaluated the software, you can get a free evaluation period by installing the software and requesting an evaluation license. How to do this and how long the evaluation period is for each software product is described in our user manuals:

CLC Genomics Workbench:
http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Request_evaluation_license.html

CLC Main Workbench: 
http://resources.qiagenbioinformatics.com/manuals/clcmainworkbench/current/index.php?manual=Request_evaluation_license.html

CLC Main Workbench and CLC Genomics Workbench without a license can be run in Viewing Mode, allowing free and easy access to extensive data viewing capabilities, basic bioinformatics analysis tools, and import and export functionality.

CLC Assembly Cell:
http://resources.qiagenbioinformatics.com/manuals/clcassemblycell/current/index.php?manual=Installing_Static_license.html

 

CLC Genomics Server

If you are interested in evaluating CLC Genomics Server, please contact bioinformaticssales@qiagen.com

 

Please see the related FAQ entry for how to get installer files for the software.

3.2. Are all features of the software available during an evaluation?

When you run CLC software using an evaluation license, you have access to the full functionality of the software.

The difference between using an evaluation license and a purchased license is that evaluation licenses expire.

When CLC Workbenches are run without a valid license, they run in "Viewing Mode". In this mode, import, export and viewing functionality is available. Please refer to the relevant manual for further information about this mode.

CLC Genomics Workbench  http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Viewing_mode.html

CLC Main Workbench http://resources.qiagenbioinformatics.com/manuals/clcmainworkbench/current/index.php?manual=Viewing_mode.html

 

Viewing Mode was introduced in CLC Genomics Workbench 11.0 and CLC Main Workbench 8.0. When older Workbenches are run without a valid license, they run in "Limited Mode". This mode allowed for less functionality then Viewing Mode. Information about Limited Mode can be found via the manual built into these Workbenches.

3.3. What happens to my data after the evaluation period if I don't purchase the software?

CLC Workbenches or Servers

Data imported or created using a CLC Workbench or Server will be in clc format.

If you plan to work on this data in the future but will not be purchasing CLC software, we recommend that you export your data to formats that will be readable by the software you plan to use. The data formats you can export to depend on the type of data you are working with and the software you are using. 

CLC Workbenches: The easiest way to view all the possible export formats is to click on the Export button in the top toolbar and scroll through the list of formats available.

CLC Genomics Server using the CLC Server Command Line Tools:  Run the clcserver command using -A export. e.g.  clcserver -S <hostname> -P <port> -U <username> -W <passcode> -A export

 

You will continue to be able to view your data via the CLC Workbench even if you do not have a valid license. To do this, start up a Workbench and choose to run in "Viewing Mode" when the message about their being no license found is presented. In Viewing mode, import, export and viewing functionality is available.

Please refer to the manual for further information about this mode.

CLC Genomics Workbench:  http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Viewing_mode.html

CLC Main Workbench: http://resources.qiagenbioinformatics.com/manuals/clcmainworkbench/current/index.php?manual=Viewing_mode.html

 

Viewing Mode was introduced in CLC Genomics Workbench 11.0 and CLC Main Workbench 8.0. When older Workbenches are run without a valid license, they run in "Limited Mode". This mode allowed for less functionality then Viewing Mode. Information about Limited Mode can be found via the manual built into these Workbenches.

 

CLC Assembly Cell

Most data remains in commonly used formats such as fasta or fastq. The main exception is the cas format outputs from read mappings. The conversion tool clc_cas_to_sam remains functional without a license, so you convert your mappings to SAM or BAM format whenever you wish to.

3.4. How can I evaluate the software on a non-networked machine?

When a evaluation license is downloaded using our standard licensing tools, as described in a related FAQ entry, the license is locked to the machine the license was downloaded to. This means that you cannot get a license for an evaluation period directly via the standard license download tools. You will need to get a license order ID for the evaluation license to proceed.

If you wish to run your evaluation on a machine that does not have a network connection, please contact bioinformaticssales@qiagen.com and let them know of your situation.

If you are then issued with a license order ID for an evaluation to be run on a non-networked machine, please see the related FAQ page for how to download a license for a non-networked machine.

4. Other contact questions

4.1. How can I sign up for notifications (e.g. new products, beta products, etc.)?

Please see the FAQ page in the Knowledge Book CLC FAQ - CLC licenses and myCLCHow can I sign up for or change subscriptions for notifications or newsletters?

4.2. How can I submit a feature request?

If you would like to submit a feature request, please write to ts-bioinformatics@qiagen.com.

We appreciate it if you can include details of what you would like to achieve with the feature you are requesting. Often, the context of the research you are doing will help us understand the request in more detail.

If you aren't sure if a particular feature is already available within our software, please check our our software manuals. You can get a pdf of our full usermanual from our usermanuals page:

https://www.qiagenbioinformatics.com/support/manuals/

There is a table of contents and an index for each of them, but you may also wish to try using the Find facility of your pdf reader for specific terms, as this can sometimes be a good way to find out if your feature of interest is already included.

4.3. How can I cite CLC Workbenches and Servers in my paper?

To cite a CLC Workbench or Server product at a general level, please cite our web site.

For example, for the Genomics Workbench version 20.0, using something along the lines of 

CLC Genomics Workbench 20.0 (https://digitalinsights.qiagen.com)

Hopefully the instructions for authors will indicate the preferences of the particular journal with regards to referencing website in this way.

 

Papers citing CLC

In case it helps in determining how to cite CLC in your paper, you can find selected papers citing CLC software on our website:

https://digitalinsights.qiagen.com/?result=citations&s=

Suggested search terms are 'Genomics Workbench', 'Main Workbench', 'Assembly Cell' or other product names.

 

Information related to specific Workbench or Server analyses

Background information relating to particular analyses can be found in our White Papers and our manual. The manuals are available in both pdf and html format. To reference a particular manual section, the html format, online manual is likely the easiest.

Application Notes and White Papers

Our Application Notes and White Papers can be found at:

https://digitalinsights.qiagen.com/science/technical-information/

For any analysis not covered by a White Paper, please refer to the manual for the product you have been using.

Manuals

Manuals for CLC software can be found online at:

https://digitalinsights.qiagen.com/technical-support/manuals/

To provide direct links to a particular section of a manual, please open the HTML version of the manual. Note though that the URL you will see at this point is for the current version of the CLC software.

If you require manual information for an earlier version, you will need to hand-edit the URL with the relevant API number. The easiest way to do this is to go to the link in the current online manual and then edit it accordingly.

Here is an example:  Let's say you wished to refer to the RNA-Seq Analysis tools of CLC Genomics Workbench 11.0.1.  If you go directly to the current webpage of the manual you are taking to:

http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Introduction_CLC_Genomics_Workbench.html

 

Notice the word current in that URL. 

Change the word "current" to the API version number, which, for the Genomics Workbench 11.0.1 is 1101. That is, the above URL should be changed to:

http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/1101/index.php?manual=Introduction_CLC_Genomics_Workbench.html

 

After which you can navigate to the section of interest, e.q.:

http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/1101/index.php?manual=RNA_Seq_Analysis_tools.html

 

We have online links for earlier version of CLC Genomics Workbench back to version 6.0 (API 600) and the Main Workbench back to version 6.7.1 (API 671). For older versions, you will need to refer to the information built into your Workbench help to get hold of the relevant manual content.