> 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/instrumentation-miseq-troubleshooting-list/000009288.md).

# Troubleshooting Stalled Flow Rate Check on the MiSeq

Users attempting to start a MiSeq run may encounter the flow rate check taking longer than expected during the Pre-Run Checks. Typically, this step takes between 3-4 minutes. However, a 10-minute flow rate check is still considered normal. If this step takes >10 minutes, this may indicate that the control software has become unresponsive.

**Troubleshooting Steps:**

1. Force-close the Control Software through the Windows Task Manager
   1. Press Ctrl+Alt+Del and select Task Manager
   2. Locate MiSeq Control Software in the Task Manager and select "End Task". This will force the control software to close.
2. Power Cycle the MiSeq. For complete instructions, review the article [How to Power Cycle the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000001894).
3. Once the system re-initializes, attempt to start the run again with the same consumables.

If the flow rate check stalls again or initialization fails, contact [Illumina Technical Support](https://www.illumina.com/company/contact-us.html#/united-states/technical-support).

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                        |
| :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #9288), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009288%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000009288.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.