Troubleshooting Focus Mirror Error on the MiSeq

The following error relates to the M3 focus mirror failing to move during flow cell scanning and leading to a premature run stop.

• This error usually mentions the M3 or focus mirror.

• If this component is not working correctly, the MiSeq will not be able to image clusters correctly.

Error Message: FocusMirror: Focus mirror move and/or sensor failed: The FPGA reported an error while executing command "FOCMRRFOC" error message: "Focus Mirror sensor not found"

Troubleshooting steps:

1. Complete the post-run wash.

2. Power cycle the MiSeq.

3. If the system initializes, run the M3 Mirror Test in the System checks 5 times to verify the mirror moving correctly.

• MiSeq Control Software (MCS) v4.0: From Main Menu, select System Check.

• MCS v3.1 and older: From Welcome Screen, select Manage Instrument, select System Check.

• Follow the prompts on the screen to start the test, and repeat the test 4 more times (5 times total).

1. If all five M3 mirror tests pass, continue with the next run.

2. If the system does not initialize or any of the M3 Mirror Tests fail, contact Illumina Technical Support for further assistance.

For further information, search for the following Knowledge Base articles:

• How to Shut down or power cycle the MiSeq

• How To Power Cycle the MiSeq Video

• System Checks for MiSeq

For any feedback or questions regarding this article (Illumina Knowledge Article #1449), contact Illumina Technical Support [e-mail].