Troubleshooting 'One or more unknown settings found' Errors during Run Planning on the NovaSeq X Series

Background

The NovaSeq X Series Control Software allows users to setup sequencing runs using the Run Planning user interface (UI). The Generate FASTQC Metrics is an optional analysis that will output various quality metrics for each sample. If this option is selected for a DRAGEN App version that is not compatible with this option when configuring multiple DRAGEN Analyses, the following error will present:

One or more unknown settings found: GenerateFastqcMetrics

Troubleshooting Actions

This error message will only present for NovaSeq X Series instruments running Control Software v1.3 when setting up runs in Run Planning using multiple Analysis configurations where at least some of the Configurations use BCL Convert versions that are incompatible with the Generate FASTQC metrics option. See the following instructions to mitigate this issue:

1. From the Run Planning UI, cancel the run setup and return to the Runs page within the NovaSeq X Series Control Software.

2. Select Create Run to restart run setup using the Run Planning UI.

3. On the Run Settings page, DO NOT select either radio button for the Generate FASTQC Metrics and leave it at the default selection.

4. Proceed with the remaining selections in Run Planning to complete Configuration setup.

5. Repeat steps 1-4 for each DRAGEN Analysis Configuration.

6. After completing Run Setup and all Configurations, see the following steps edit the Generate FASTQC Metrics selection if needed:

   1. Under the Planned Runs tab, select the Run to edit.

   2. In the Run Review page, select Edit in the bottom-right corner.

   3. For the select the Edit link. next to the Configuration # that requires updating.

   4. Under Analysis Settings, select the appropriate radio button for the desired Generate FASTQC Metrics option.

   5. Select Save.

   6. Select Save as Planned.

For any feedback or questions regarding this article (Illumina Knowledge Article #9387), contact Illumina Technical Support [e-mail].