Troubleshooting camera, cluster, and focus errors at cycle 1 on the MiniSeq

The following notification types indicate that the MiniSeq is unable to detect clusters at cycle 1. Cycle 1 errors can occur due to instrument, consumable, or library (design/custom primers/quantification/denaturation) causes.

Potential error messages include:* Camera 1 disabled

• Failure to Detect Clusters

• Failed to generate focus model for the top surface

  

Note 1: A pop-up in the Control Software may appear asking if the user would like to save the flow cell. Select No, as the flow cell cannot be re-used.

Note 2: The instrument gives an option to purge reagents after the run ends. This option will proceed with purging consumables, then performing the automatic post-run wash. The purging process can take a few hours (especially for a cycle 1 error because most of the reagents are still in the reagent cartridge). The purge is optional and can be bypassed if desired.

Troubleshooting steps:

1. Acknowledge the error message.

• The flow cell cannot be saved.

• Illumina does not require the reagent purge.

2. Perform the post-run wash.

3. Power cycle the instrument.

• For further information, search for Knowledge Base article How to Power Cycle the MiniSeq.

4. Perform the System Check with a used flow cell.

• For further information, search for Knowledge Base article How to Perform a System Check on the MiniSeq.

• If the System check fails, Contact Illumina Technical Support.

5. If the System Check passes, the failure may be due to an issue with the library or reagents. To investigate the most common issues:

• Check reagent kits for expiration dates and proper storage.

• Make sure the library design is compatible with running on Illumina platforms.

• Check the quality and quantification of the library using Illumina-recommended methods.

• Check the denaturation steps.

• Make sure any custom sequencing primers are compatible with the 60°C annealing temperature for the MiniSeq.

• Make sure any custom sequencing primers were added to the correct cartridge wells at the proper concentration.

If there are no apparent issues with the library or reagents, repeat the run with a 20% PhiX control spike in. This will act as a positive control for clustering for the next run to determine if an underlying library issue caused the previous error.

If an error occurs at cycle 1 of the next run, contact Illumina Technical Support at [e-mail] for further assistance.

For any feedback or questions regarding this article (Illumina Knowledge Article #1198), contact Illumina Technical Support [e-mail].