How to resolve 'Critical System Error: An unexpected error has occurred with system integration' during initialization on the NovaSeq X/X Plus

Issues with the NovaSeq X Series Control Software connecting to the onboard Compute Engine (CE) will result in a Critical System Error during initialization.

Error message: “Critical system error: An unexpected error has occurred with system integration. Power cycle the instrument per system guide instructions and retry. If the issue persists, please contact Illumina Technical Support.”

If this error presents on the NovaSeq X/X Plus, see the following.

Troubleshooting steps:

1. Contrary to the error statement, do not power cycle the instrument.

2. Exit the NovaSeq X Series Control Software and wait 10 minutes, then restart the NovaSeq X Series Control Software.

3. If the issue persists, power cycle the instrument.

   1. For power cycling instructions, see the How to power cycle the NovaSeq X/X Plus article in Illumina Knowledge.

4. After logging into the Linux Operating System (OS), wait at least 15 minutes before starting the Control Software.

5. If the issue persists after power cycling, contact Illumina Technical Support.

For any feedback or questions regarding this article (Illumina Knowledge Article #7766), contact Illumina Technical Support [e-mail].