Troubleshooting "Y home sensor never tripped" error on MiSeq

The MiSeq may give the error "Y stage encountered homing error when MiSeq was doing “Home All” function" or “Y home sensor never tripped" during MiSeq Control Software (MCS) initialization or during a run. This error will likely cause an ongoing run or initialization to fail.

Troubleshooting steps:

1. Perform the post-run wash if the run stops or after the run is completed.

2. Power cycle\* the MiSeq.

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

• Make sure that a used flow cell is loaded on the instrument (the same wash flow cell is okay).

• Select Y Stage test.

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

  • MCS 3.1 and older: From the Welcome Screen, select Manage Instrument, then select System Check.

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

4. If all Y Stage tests pass, continue with normal sequencing.

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

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

• \*How to shut down or power cycle the MiSeq.

• \*How To Power Cycle the MiSeq Video.

• How to perform a System Check on the MiSeq.

For any feedback or questions regarding this article (Illumina Knowledge Article #2353), contact Illumina Technical Support [e-mail].