How to perform a NextSeq 500/550 system check

Important Note: For the system checks launched from NextSeq Control Software (NCS) 4.0 and newer, the NextSeq Service Software (NSS) will present a login screen. This requires any Local Run Manager (LRM) account credentials.

Performing the System Checks on the NextSeq 500/550

1. Navigate to the Home screen in NextSeq Control Software (NCS).

2. Select Manage Instrument > System Check, then select yes to service software opening.

3. If prompted, input the Local Run Manager (LRM) username and password.

4. When prompted by the instrument, load the following consumables:

   1. A used high output flow cell (a high output flow cell is strongly recommended, as mid output flow cells can lead to false flow rate failures).

   2. An empty spent reagents tray.

   3. A wash buffer tray with 150 ml of lab-grade water in the center reservoir.

   4. An empty wash reagent tray.

5. The tests will be pre-selected. Do not select unchecked tests, as the unchecked tests can only be performed by Illumina personnel.

6. Select Next to start the System Check. The System Checks will take about 90 minutes to complete.

   1. Passing system checks are indicated with green checkmarks and a PASS record for the test.

7. The results of the tests are saved to D:\Illumina\SystemCheckResults\<Test Name>\<Date of Test>. Collect this folder and provide it to Illumina Support teams for further review.

   1. A screenshot of the results summary screen is also helpful for Illumina Support.

Note: The new NextSeq 550 wash wash cartridge has a label listing the minimum (150 ml) and maximum allowable volumes. The previously recommended volume of 120 ml as listed in the NextSeq 550 system guide is safe to use instead of the 150 mL listed above.

For any feedback or questions regarding this article (Illumina Knowledge Article #1883), contact Illumina Technical Support [e-mail].