> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/instrumentation/miniseq/instrumentation-miniseq-reference_material-list/000002040.md).

# How to Perform a System Check on the MiniSeq

**The MiniSeq System Check process requires the following.**

* One wash flow cell (a previously used flow cell; this wash flow cell can be either a mid output or high output used flow cell. ).
* One wash cartridge filled with 40 ml lab-grade water (loaded in well 40 as indicated below).

  ![](/files/jEz3VoGJvewRshjqCZQX)

**To perform the system check on the MiniSeq:**

1. Navigate to the Home screen in the MiniSeq Control Software (MnCS).
2. Select **Manage Instrument**→**System Check**.\
   a. MnCS automatically closes to allow the MiniSeq Service Software (MnSS) to launch.
3. Perform the following steps (the instrument does **not** prompt this).

a. Load a wash flow cell (used flow cell).

b. Empty the spent reagent bottle and return it to the instrument.

c. Load a wash tray with 40 ml lab-grade water in the wash reservoir, position #40. (Note: The MnSS may present the prompt "Fill in BB3 with DI water prior the test. Re-insert wash tray, then press OK". The BB3 position is the same as well position #40).

4. The following tests are pre-selected (the unchecked tests are those performed by Field Service Engineers only).

Motion: FCLM & FAM, Stage Test\
Optics: Flow cell Registration\
Fluidics: Valve response, Pressure decay, Flow rate\
Thermal: Fans, Thermal probes

5. Select **Next** to begin the system checks.

The system checks require manual input about 5-10 minutes after the check start during the pressure decay test.

The checks take approximately 20 minutes to complete.

Once the test completes, a read-out of each test showing Pass or Fail result appears on the screen.\
If any of the tests fail, contact Illumina Technical Support at <techsupport@illumina.com> and provide the System Check results from D:\Illumina\SystemCheckResults\SystemCheckResultsDetails.csv.\
After reviewing the results, select **Exit** to close the MiniSeq Service Software and return to MiniSeq Control Software.

\
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| *For any feedback or questions regarding this article (Illumina Knowledge Article #2040), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002040%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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