Troubleshooting "Compensator Move and/or Sensor Failed" errors on the MiSeq

Users may encounter a compensator error during a MiSeq run, system check, or Control Software initialization. This error indicates that the compensator on the instrument, which allows the cameras to change focus between the top and bottom of the flow cell, is not functioning properly. This can be the result of a communication error on the instrument or may indicate a hardware issue on the instrument.

Error message: Compensator Move and/or Sensor Failed on retry #3 /3: Moving to OutOfPath, StartCurrent =...

Troubleshooting Steps:

1. Perform the post-run wash.

2. Power cycle the MiSeq.

3. If no issues with re-initialization, perform the Compensator test 5 times.

   1. Start system check with used flow cell is loaded on the instrument (the same wash flow cell should be okay).

   2. Select Compensator test.

      1. MiSeq Control Software (MCS) v 4.0: From Main Menu, select System Check.

      2. MCS 3.1 and older: From Welcome Screen, select Manage Instrument, select System Check.

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

4. If all Compensator test replicates pass, continue with normal sequencing.

5. If the system fails to initialize or any of the 5 replicates of the Compensator test fail, contact Illumina Technical Support for further assistance.

For further information, see the following Knowledge Base articles:

• How To Power Cycle the MiSeq Video

• System Checks on MiSeq

For any feedback or questions regarding this article (Illumina Knowledge Article #8020), contact Illumina Technical Support [e-mail].