Troubleshooting a Software Shutdown Issue Warning on the NextSeq 500/550 with NCS 4.0.X

The following message may appear when shutting down or restarting the NextSeq 500/550 and can be associated with Proactive being enabled. This warning does not affect run quality or system performance.

"Software shutdown issue(s): Data from the previous sequencing run is being sent to persistent storage. Select Cancel to wait for the transfer to finish. Do you want to proceed?"

Troubleshooting steps:

1. If the instrument not connected to the internet, disable Proactive monitoring as follows:

   1. Navigate to the NextSeq Control Software.

   2. Select System Settings.

   3. Deselect the option Send Instrument Performance Data to Illumina.

2. If all runs have completed transfer and/or upload, apply instructions found in the following article: Troubleshooting Universal Copy Server error on the NextSeq 500/550 (NCS 4.0+).

3. If the most recent run is still being transferred and/or uploaded, it is acceptable to select Proceed and ignore the message.

   • If run data had not finished copying, Universal Copy Service (UCS) will continue process after instrument has been restarted.

For any feedback or questions regarding this article (Illumina Knowledge Article #2449), contact Illumina Technical Support [e-mail].