Lost connection with server error on the NextSeq 1000/2000

If there is a System Failure: Lost connection with Server error on the NextSeq 1000/2000 instrument while the instrument is sequencing, DO NOT select "Yes, I'm finished".

Most often, the run continues sequencing even if it is not displayed on the control software.

To check that the run is still sequencing:

1. Minimize the control Software.

2. Open the file navigation system and navigate to /usr/local/illumina/runs/[run folder]/Data/Intensities/BaseCalls/L001

3. Check date and time stamps to see if new files and folders are being created.

When the run completes, close the control software and re-initialize it. Power cycle the instrument before starting the next run.

For instructions on how to power cycle the instrument, see: How to power cycle the NextSeq 1000/2000

If the run completes successfully but the run is listed as Errored in Process Management, reach out to Technical Support for help generating FASTQ files.

For any feedback or questions regarding this article (Illumina Knowledge Article #8547), contact Illumina Technical Support [e-mail].