# How to troubleshoot “Some of the settings may not be available when system activity is in progress” during run setup in MiSeq i100 Series

In some cases, after selecting the run “Start” screen (**Figure 1**), users may need to perform setting adjustments. For example, if the incorrect BaseSpace instance was selected or if a USB must be mounted for accessing a sample sheet.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-9ad9752cd8f826148a38b07642eff26d787f83b4%2Fimage1.png?alt=media)

**Figure 1.** Screen displayed after clicking Start from the MiSeq  i100 Series Control Software main menu.

If the Settings tab is opened after initiating Run Setup by selecting **Start**, the Control Software may display the warning message “Some of the settings may not be available when system activity is in progress”, and several settings options are unavailable (grayed out) (**Figure 2**).

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-324fcef425639dcd320e396149f8b42d256e431f%2Fimage2.png?alt=media)

**Figure 2.** Settings screen showing grayed-out options and the warning message at the bottom of the screen.

This behavior can occur when the user attempts to access the Settings option from the left‑hand menu while in run setup. When **Start** is selected, the system immediately enters the run setup state, treats it as an active process, and limits the available settings options. To remove this warning and restore full access to the Settings menu, select the **Back** arrow (see Figure 1, left arrow) to exit run setup and re-enable all Settings options.

If the warning remains visible after exiting run setup, check the Runs Active tab for any ongoing background processes (e.g., data uploads or in-progress analyses) that may temporarily restrict access to certain settings.

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