How to perform System Checks on the NovaSeq X Series

Background

The NovaSeq X Control Software v1.3 and above allows users to perform select System Checks within the Control Software. These checks cover Fluidics, Precision Motion, and Reagent Buffer Assembly (RBA) movement systems.

These checks can be used to assess instrument performance when recommended by Illumina Support teams as part of troubleshooting. However, system checks should only be performed when recommended by Illumina Support teams and not used as part of routine maintenance.

A wash flow cell or a used 8-lane sequencing flow cell that has not been removed from the instrument after the previous run can be used for the system checks. The Control Software will not add one use to the wash flow cell counter if using the wash flow cell.

The complete system checks take approximately 2 hours in total (Fluidics: ~01:39 / Precision Motion: ~00:18 / RBA Movement: ~00:06).

Important note: Always exit and restart the Control Software when the System Checks are complete.

Limitations

• Control Software v1.3.x - System checks must be run on both sides of the NovaSeq X Plus instrument even when troubleshooting a single side.

  • Control Software v1.4 and above allow running single-sided checks on NovaSeq X Plus instruments where applicable.

  • For the single-sided NovaSeq X instrument, the system check is only performed on side A.

• The user can specify which check categories to perform, though all checks within each category must be performed.

Setting up the System Checks

1. From the NovaSeq X Series Control Software Home screen, select the instrument icon to open the global navigation menu.

2. Select Settings, and then System Checks (Figure 1).

3. Select the checkbox for the system checks to perform (Figure 2).

   1. Fluidics: Will check the performance of the fluidic system

   2. Precision motion: Will check the travel limits and performance of the Z-stage and XY-stage

   3. RBA movement: Will check if the RBA mechanism is working properly

   4. Note:wash consumables are required for the Fluidics and RBA checks

4. If performing Fluidic checks, prepare the used buffer cartridge as follows:

   1. Empty the used buffer cartridge in accordance with the applicable environmental health and safety (EH&S) standards.

   2. Rinse the middle well of the buffer cartridge (TB2 position) with laboratory-grade water at least three (3) times.

      1. Important note:Rinsing the buffer cartridge prevents damage to the flow rate sensor that is used during the fluidic checks.

   3. Fill the middle well of buffer cartridge (TB2 position) halfway with laboratory-grade water and load the prepared buffer cartridge.

5. Select Load consumables.

6. Load a wash flow cell or use a used 8-lane sequencing flow cell that has not been removed from the instrument after the previous run.

7. Load an empty wash reagent cartridge.

8. Load the prepared or empty used buffer cartridge as follows:

   1. [Fluidics and any other Checks] Prepared buffer cartridge.

   2. [RBA movement/Precision motion ONLY] Empty buffer cartridge.

9. Empty the used small and large spent reagent bottles in accordance with the applicable EH&S standards for each region.

10. Select Start checks.

11. Once checks have completed, exit and restart the Control Software application.

    1. Select the instrument icon to open the global navigation menu.

    2. Select Settings, then select Exit Application.

    3. From the Linux Operating System (OS), select Activities in the top-left corner.

    4. Select the NovaSeq X Series Control Software icon to relaunch the Control Software.

12. Once Control Software has initialized, perform a Maintenance Wash if the instrument will remain idle for more than two (2) days before the next sequencing run.

When completed, the system checks will display the results of each check and the results are output to /usr/local/illumina/system-checks. If requested, collect the results files from this location on the instrument and provide them to Illumina Support teams for review.

Figure 1. Settings menu highlighting the System checks option.

Figure 2. System Checks selection menu used to select which Checks to perform.

For any feedback or questions regarding this article (Illumina Knowledge Article #9317), contact Illumina Technical Support [e-mail].