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