# Troubleshooting Flow Cell Thermal Errors during Pre Run Checks on the MiSeq i100 Series

**Background**

The MiSeq i100 performs Pre-Run Checks (PRC) at the start of each run to ensure that the instrument and consumables are ready to start the sequencing run. Issues with initializing the CMOS sensor on the flow cell or performing the Flow Cell Thermal PRC result in the following error:

There was a problem with the flow cell thermal checks.

If this error presents during the Pre-Run Checks on the MiSeq i100 Series instrument, see the following steps to Troubleshoot.

**Troubleshooting Actions**

1. If available, select the **Retry** button and monitor if the Pre-Run Checks complete on the second attempt.
2. If the issue persists, **power cycle** the instrument to reset any potential communication issues.
   1. See Knowledge Article [How to Power Cycle the MiSeq i100 Series](/instrumentation/miseq-i100-series/instrumentation-miseq-i100-series-reference_material-list/000009277.md) for additional details if required.
3. If the instrument initializes as expected, attempt run setup again using the **same consumables**.
4. If the Pre-Run Check error persists, perform the instrument **System Health Checks** according to Knowledge Article [How to Setup the System Health Checks on the MiSeq i100 Series Instruments](/instrumentation/miseq-i100-series/instrumentation-miseq-i100-series-reference_material-list/000009206.md).
   1. If the System Health Checks are **PASS**, repeat sequencing run setup using a new Dry Cartridge.
   2. If the System Health Checks do not pass, unload the **Dry Test Cartridge (DTC)** and gently clean the top and bottom of the flow cell (FC) using compressed air and a 70% isopropyl alcohol (IPA) solution with a lint-free wipe. Repeat System Health Checks.

If the System Health Checks continue to fail or the Pre-Run Check errors persist after replacing the Dry Cartridge, contact [Illumina Tech Support](https://www.illumina.com/company/contact-us.html) for further assistance.

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                        |
| :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #9459), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009206%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


---

# Agent Instructions: 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-i100-series/instrumentation-miseq-i100-series-troubleshooting-list/000009459.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.