Pre Run check failed with an alignment check failure on the NextSeq 1000/2000

Error notification in Control Software: "An alignment check failed. Reload the flow cell and retry the pre-run check. If the problem persists, contact Illumina Technical Support."

If this error occurs during the dry pre-run checks, the consumables are not marked as used.

Troubleshooting steps:

• If this error occurs, reseat the flow cell and repeat the pre-run checks.

• If error persists, attempt pre-run checks with a different flow cell.

  • If resolved by a new flow cell, the flow cell quality is the suspected root cause. Provide the lot and serial number to Illumina Technical Support for replacement.

• If error persists with alternative flow cell, collect the following Logs and contact Illumina Technical Support for file transfer link and next steps:

  • NextSeq 1000/2000 control software logs: /usr/local/Illumina/logs/nextseq1k2k-control-software

  • Pre-run check logs: usr/local/Illumina/Runs/Setup/[Date_Time]

For any feedback or questions regarding this article (Illumina Knowledge Article #3529), contact Illumina Technical Support [e-mail].