How to troubleshoot flow cell clamp or vacuum is unable to engage errors when loading flow cells on the NovaSeq 6000

During NovaSeq 6000 run setup, it is possible to see one or more of the following errors when loading a flow cell:

The flow cell clamp is unable to engage. Load or reseat the flow cell.
The flow cell vacuum is unable to engage. Load or reseat the flow cell.
RFID cannot be read.
Consumable loading problem. Reload consumables or contact Technical Support for help.

Troubleshooting Steps:

Acknowledge the error. This will open both the flow cell and reagent doors.
Clean the bottom of the flow cell and flow cell stage with an alcohol wipe and a dry, lint-free wipe to remove any debris on these surfaces.
- For more information on how to clean the flow cell and flow cell stage, search for Knowledge Base article Troubleshooting NovaSeq 6000 flow cell loading issues Video.
If the issue persists, attempt to load a wash flow cell.
If the wash flow cell is unable to be read/engaged, power cycle the instrument and try the wash flow cell again.
- For more information on how to power cycle the instrument, search for Knowledge Base article How to Power Cycle the NovaSeq 6000 System?
If the wash flow cell engages after the power cycle, try the original flow cell again.
If the issue is not resolved by cleaning/reseating, using a new flow cell, or power cycling the instrument, measure flow cell vacuum pressure as instructed below and contact Illumina Technical Support for the next steps.

Checking flow cell vacuum pressure in NovaSeq Service Software (NVSS):

Close the NovaSeq Control Software and launch NovaSeq Service Software (NVSS).
Once initialized, select the Flow Cell option on the main screen.
Load S3 Wash Flow Cells on Sides A and B.
Pressure readings should be around -90 kPa for wash flow cells and show a steady green check mark for the sensor.
If pressure is low or the sensor is not steady, can try cleaning the flow cell and stage one more time and measuring pressure.
Contact Illumina Technical Support with results.

Last updated 4 months ago

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During NovaSeq 6000 run setup, it is possible to see one or more of the following errors when loading a flow cell:

The flow cell clamp is unable to engage. Load or reseat the flow cell.
The flow cell vacuum is unable to engage. Load or reseat the flow cell.
RFID cannot be read.
Consumable loading problem. Reload consumables or contact Technical Support for help.

Troubleshooting Steps:

Acknowledge the error. This will open both the flow cell and reagent doors.
Clean the bottom of the flow cell and flow cell stage with an alcohol wipe and a dry, lint-free wipe to remove any debris on these surfaces.
- For more information on how to clean the flow cell and flow cell stage, search for Knowledge Base article Troubleshooting NovaSeq 6000 flow cell loading issues Video.
If the issue persists, attempt to load a wash flow cell.
If the wash flow cell is unable to be read/engaged, power cycle the instrument and try the wash flow cell again.
- For more information on how to power cycle the instrument, search for Knowledge Base article How to Power Cycle the NovaSeq 6000 System?
If the wash flow cell engages after the power cycle, try the original flow cell again.
If the issue is not resolved by cleaning/reseating, using a new flow cell, or power cycling the instrument, measure flow cell vacuum pressure as instructed below and contact Illumina Technical Support for the next steps.

Checking flow cell vacuum pressure in NovaSeq Service Software (NVSS):

Close the NovaSeq Control Software and launch NovaSeq Service Software (NVSS).
Once initialized, select the Flow Cell option on the main screen.
Load S3 Wash Flow Cells on Sides A and B.
Pressure readings should be around -90 kPa for wash flow cells and show a steady green check mark for the sensor.
If pressure is low or the sensor is not steady, can try cleaning the flow cell and stage one more time and measuring pressure.
Contact Illumina Technical Support with results.

For any feedback or questions regarding this article (Illumina Knowledge Article #3046), contact Illumina Technical Support .