Troubleshooting flow cell registration failed to find fiducial on the NextSeq 500/550

This notification indicates a fiducial was not found during flow cell registration. The fiducial measures a baseline X and Y distance between each of the cameras relative to camera 2. It is designed to detect gross misalignment between cameras. The XY registration test is performed to find the fiducial on the flow cell, which occurs before the run starts during the pre-run checks. The cameras do not reference the fiducial during sequencing runs, and a failing XY registration test does not correlate to a run failure.

Fiducials do not require clustering for detection the NextSeq 500/550. These notifications do not affect run performance and are transient communication issues. The NextSeq 500/550 flow cell has 6 fiducials and the instrument requires reading of 1 to start the run.

Example notification in NextSeq 500/550 Control Software

Troubleshooting steps:

1. Allow the run to start.

2. After the run completes, confirm run performance was not affected by the error.

3. Power cycle\* NextSeq 500/550.

4. If the system initializes without issue, proceed with the next sequencing run.

\*For further information, search for Knowledge Base Article How to Perform a NextSeq 550 Power Cycle.

For any feedback or questions regarding this article (Illumina Knowledge Article #1383), contact Illumina Technical Support [e-mail].