Troubleshooting Z motor errors occurring mid run on the MiSeq

A Z motor error occurring mid-run can be caused by instrument fluidics, debris, smudges on the flow cell, or library overclustering issues.

ERROR: While trying to find focus, the Z stage has attempted to move outside its acceptable range.

Troubleshooting steps:

1. Confirm reagent kits were not expired at the time of the run.

2. Confirm the quality and quantification of the library were as expected and were checked in accordance with Illumina-recommended methods.

3. Contact Illumina Technical Support with the following run files to review the library performance.

   1. From within D:\Illumina\MiSeqTemp<run folder>, send: InterOp folder RunParameters.xml RunInfo.xml Thumbnail_Images\L001\C1.1 (cycle 1)\* \*Send cycles 1-10 and the last 10 cycles before the run failed.

4. Power cycle\* the instrument.

5. If the instrument initializes successfully, perform a System Check on the instrument.

6. If the system check passes and Technical Support does not suspect a library-related issue, proceed with setting up the next run.

7. If Z motor error recurs in the subsequent run, contact Illumina Technical Support.

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 on Miseq.

For any feedback or questions regarding this article (Illumina Knowledge Article #1850), contact Illumina Technical Support [e-mail].