Troubleshooting a flow cell registration stall during pre check on first run on NextSeq 500/550

On the first run after upgrading the NextSeq 500/550 to NextSeq Control Software (NCS) v4.0.X, the pre-run checks can take around 30 minutes to complete the flow cell registration. This is expected as the instrument will be downloading drives to perform the check.

Allow the pre-run check to continue as long as no errors appear.

If an option comes up to retry the pre-check, this can indicate a communication issue. This can be resolved by re-seating the flow cell and power cycling the instrument.

For further information, search for Knowledge Base article How to Perform a NextSeq 500/550 Power Cycle.

For any feedback or questions regarding this article (Illumina Knowledge Article #2112), contact Illumina Technical Support [e-mail].