Troubleshooting "Instrument Shell has Stopped Working" on the NovaSeq 6000

The "Instrument Shell has Stopped Working" error on the NovaSeq 6000 is a Windows error that generally indicates transient communications issues or hardware problems. This error will manifest as the Control Software crashing, and the pop-up shown below appearing on the screen.

Instrument Shell has stopped working. A problem caused the program to stop working correctly. Please close the program.

• Close the program

• Debug the program

  

To Troubleshoot:

• Power cycle the instrument. For further information, search for Knowledge Base article How to Power cycle the NovaSeq 6000 System.

• Collect the following files:

  • NovaSeq Control Software logs folder: C:\ProgramData\*\Illumina\NovaSeq\NovaSeq Control Software\Logs (zipped)

  • Windows logs - After collecting the logs, contact Illumina Technical Support ([e-mail]) to determine the next steps.

For any feedback or questions regarding this article (Illumina Knowledge Article #6676), contact Illumina Technical Support [e-mail].