Troubleshooting "Unable to Generate a Focus Model" error on the NovaSeq 6000

Error message:

"Unable to generate a focus model for the flow cell, which requires an onsite correction. Contact Technical Support for help."

Figure 1. Example Error message in NovaSeq Control Software

The focus model is generated by the Focus Tracking Module (FTM) and Line Generation Module (LGM). The FTM is a secondary onboard laser diode separate from main Red and Green lasers of the LGM. Failure to generate a focus model is related to either low intensities of the lasers on the Focus Tracking Module (FTM), a consumable issue with the flow cell, fluidics, temperature, or other optical issues.

Troubleshooting steps:

1. Power cycle the instrument.

   1. For more information, review the Knowledge Base article How to Power Cycle the NovaSeq 6000.

2. Once the instrument initializes successfully, perform a system check.

   1. For more information, review the Knowledge Base article How to perform system checks on the NovaSeq 6000.

3. Inspect the flow cell for any debris/glass shards or defects.

4. Collect the following files and contact Illumina Technical Support ([e-mail]) for instructions on how to upload the compressed Alignment folder to a secure site for review and next steps.

   1. Logs folder: C:\ProgramData\Illumina\NovaSeq\NovaSeqTemp[Run_Folder]\Logs

   2. Alignment folder: C:\ProgramData\Illumina\NovaSeq\NovaSeqTemp[Run_folder]\Alignment

For any feedback or questions regarding this article (Illumina Knowledge Article #1306), contact Illumina Technical Support [e-mail].