Troubleshooting "Would you like to include the first time setup results…?" on NextSeq 500/550

The Windows 10 upgrade for the NextSeq 500/550 adds a feature that allows the 'instrument setup .csv' file to be added to the run folder.* The 'instrumentsetup.csv' file contains information from the initial instrument set up.

• This message and file have no impact on runs regardless of the choice that is chosen.

Upon run completion, NextSeq Control Software shows the message:

• "Your input is needed. Would you like to include the first-time setup results with this run?"

• The options given are: 'Yes', 'No', and 'Don't ask again.'

This message is expected and does not affect sequencing.

• If the user selects 'Yes', the 'instrumentsetup.csv' file will be added to the run folder; the instrument will proceed to the post-run wash, and the message will show up again on the next run.

• If the user selects 'No' the 'instrumentsetup.csv' file will not be added to the run folder; the instrument will proceed to the post-run wash, and the message will show up again on the next run.

• If the user selects 'Don't ask again' the prompt will not show up again and the instrument will proceed to the post-run wash.

For any feedback or questions regarding this article (Illumina Knowledge Article #2377), contact Illumina Technical Support [e-mail].