# Troubleshooting System Configuration errors during Pre Run Checks on the MiSeq i100 Series

**Background**

The Pre-Run Checks assess whether the instrument is prepared for performing a sequencing run. As part of this, the system pulls the appropriate configuration files based on the consumable kits that are loaded into the instrument for this run. If there are issues with collecting these files, the following error presents in the Control Software: "Pre-Run checks errors: There was a problem with the system configuration. Contact Illumina Technical Support for help."

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-b2ae4284d2fe0d037884c38de7dd784ecca8400b%2Fimage1.png?alt=media)

If this issue presents during the Pre-Run Checks, please see the following Troubleshooting Actions.

**Troubleshooting Actions**

If there is an issue with the system configuration during Pre-Run Checks, first select the **Retry** button. If the error persists, see the following recommendations:

1. Select **Return to Start** to return to the MiSeq i100 Series Control Software home screen.
2. Perform the instrument **System Health Checks**.
   1. Select only the **Optics and flow cell thermal** checkbox.
   2. See Knowledge Article [How to Setup the System Health Checks on the MiSeq i100 Series Instruments](https://knowledge.illumina.com/instrumentation/miseq-i100-series/instrumentation-miseq-i100-series-reference_material-list/000009206) for additional details.
3. If the Optics Checks are all **PASS**, issue is likely due to the Dry Cartridge. Repeat run setup using a new Dry Cartridge, though the previous Wet Cartridge can be used.
4. If there are issues with any of the Optics checks, **power cycle** the instrument.
   1. See Knowledge Article [How to Power Cycle the MiSeq i100 Series](https://knowledge.illumina.com/instrumentation/miseq-i100-series/instrumentation-miseq-i100-series-reference_material-list/000009277) for additional details.
5. If the instrument is able to initialize successfully, repeat the **System Health Checks**, selecting only the **Optics and flow cell thermal** checkbox.
6. If the Optics checks are now PASS, proceed with repeat sequencing run setup using the **SAME** Dry and Wet cartridges from initial run setup attempt.

If the Pre-Run Checks or Optics checks continue to present issues, 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 #9287), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009287%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |