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", as this closes the Control Software and stops the run if it is ongoing.

Most often, the run continues sequencing even if it is not displayed on the control software. Please see the following instructions to check if the run is still going or if it has been completed:

To check that the run is still sequencing:

1. Minimize the Control Software (if the three-line menu is not accessible, use the "Windows key + H" or "Alt + Spacebar" shortcuts)

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 verify if new files and folders are being created

To check that a run is completed:

1. Minimize the Control Software

2. Navigate to the output folder configured for the run

3. Check for the presence of the "CopyComplete.txt" file

When the run completes, close the control software and re-initialize (selecting "Yes, I'm finished" will close the Control Software). 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].