Troubleshooting System File errors during pre run checks on the NextSeq 1000/2000

Background

During Pre-Run Checks, the NextSeq 1000/2000 verifies the Recipe files on instrument are compatible with the version of the reagent cartridge and flow cell that have been used to start the sequencing run.

If there are issues with locating or compiling the Recipe files, the following error will present during the Pre-Run Checks:

"Pre-Run Checks failed due to a system file issue. Contact Illumina Technical Support."

Resolution steps

If this error presents during the pre-run checks, this is often due to the Control Software not being compatible with the particular kit type. To resolve the issue, update the NextSeq 1000/2000 Control Software Suite to the latest version. See the following page for control software downloads.

NextSeq 1000/2000 Control Software Suite Downloads

See the following Knowledge article for guidance on storing the reagent cartridge and flow cell during the upgrade process.

Thawing and reagent preparation guidelines for the NextSeq 1000/2000 reagents

Once the Control Software upgrade is complete, proceed with setting up a new sequencing run using the same consumables (as long as they are within the recommended storage time after thawing). See Returning NextSeq 1000/2000 reagents to storage for more information on storage time for opened consumables.

If the Control Software Suite has already been upgraded or the issue persists after upgrade, contact Illumina Technical Support for further assistance.

For any feedback or questions regarding this article (Illumina Knowledge Article #9048), contact Illumina Technical Support [e-mail].