> 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/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000001890.md).

# Troubleshooting frozen MiSeq Control Software

**Background**

The MiSeq Control Software (MCS) may freeze if the instrument has not been power cycled or has been left idle for an extended period

**Troubleshooting**

1. If the system seems frozen during a run, **listen** to determine whether any of the MiSeq motors are being used for sequencing. This manifests as clicking or whirring sounds.
2. If noises **can** be heard, it is most likely that the run is still proceeding.
   * Let the run continue.
3. If there are no noises coming from the MiSeq after several minutes, try one of the following options:
   1. If the MCS does not close by selecting X in the upper right corner, \*\*press "\*\*CTRL+ALT+DEL" to open **Task Manager**. Right-click **MiSeq Control Software** and **End Process.**
   2. Perform a **power cycle** on the instrument following the steps in [How to Power Cycle the MiSeq](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000001894.md) or [How To Power Cycle the MiSeq Video](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000005871.md).
4. If the MCS still does not close, perform a **hard reboot** by turning off the system by the power switch on the back, right side of the instrument.
   * **NOTE:** This is the least desirable option and should only be used if the MCS will not close using the previously described methods.
   * Leave the system off for about 5 minutes, then **toggle** the power switch to turn it back on.
   * If the system fails to boot or MCS fails to initialize after a hard reboot, perform an **additional power cycle**.
5. If after the above steps there are still issues with system reboot or MCS initialization, **contact** [Illumina Technical Support](https://www.illumina.com/company/contact-us.html#/) for further assistance.

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #1890), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001890%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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