How to resolve Network Connection warnings during Pre Run Checks on the NovaSeq X Series

Background

During Pre-Run Checks, the NovaSeq X Series instruments perform checks to verify the instrument is ready to perform a sequencing run. One of the first checks performed is verifying that External or Cloud Storage locations are accessible, and the instrument has the appropriate read/write permissions.

If there are issues with this connectivity check, the following warning presents to the user:

Warning: The run data will not be copied to the network, and will need to be copied to the network folder manually.

If this Warning presents during Pre-Run Checks, see the following troubleshooting steps.

Troubleshooting Actions

1. The Warning message will present the option for the user to select Continue and proceed with the Pre-Run Checks.

• Important: If this option is selected, the Control Software will not automatically transfer the run data to External or Cloud Storage and the data will need to be transferred manually.

  • For External Storage locations, see Knowledge Base Article How to access network storage locations in Linux on the NovaSeq X Series for instructions on how to mount a network share for manual data transfers.
  • For Cloud Storage, see Knowledge Base article Using the BaseSpace Command Line Interface (CLI) Tool on the NovaSeq X Series for instructions on how to upload data to BaseSpace.

1. Alternatively, select Return to Start and see Troubleshooting Actions for both External and Cloud Storage connectivity below, then retry the Pre-Run Checks.

Testing External Storage Connectivity

1. From the NovaSeq X Series Home screen, select the instrument icon, then select the Settings menu, then select External Storage.

2. On the External Storage User Interface (UI), select the Server Location that failed during the Pre-Run Checks.

3. Review the share path in the Server Location to ensure that it is accurate.

4. Perform the Test Configuration check:

   1. For SMB Shares: Input the password for the network storage location and then select Test Configuration.

   2. For NFS Shares: No additional input required, select Test Configuration to start the check.

5. If the check is successful, select Save and return to the Settings menu.

   1. If the Test Configuration check fails, contact Illumina Technical Support.

Testing Cloud Settings Connectivity

1. From the NovaSeq X Series Home screen, select the instrument icon, then select the Settings menu, then select Cloud Settings.

2. Check instrument Cloud Connectivity settings are configured properly:

   1. If instrument is NOT connected to the internet, ensure that all Cloud Connectivity checkboxes including Proactive Support are de-selected. In the Hosting Location dropdown, select the blank entry at the top of the list.

   2. If instrument is connected to the internet and is expected to upload data to Proactive or BaseSpace, ensure the appropriate Hosting Location and Cloud upload checkboxes are selected.

3. For connected system, select Test Configuration to verify that all required URL endpoints are accessible.

   1. If any URLs are not accessible, discuss with your local IT team to ensure that network security settings are configured to allow these connections.

After verifying both External Storage and Cloud Settings Connectivity checks are passing, proceed with repeating Run Setup and Pre-Run Checks. If network connection warning persists, contact Illumina Technical Support.

For any feedback or questions regarding this article (Illumina Knowledge Article #8308), contact Illumina Technical Support [e-mail].