Troubleshooting Insufficient Storage Space Errors during Pre Run Checks on the NovaSeq X Series

Background

The NovaSeq X Series instrument is designed to output data to a networked storage location, though the data is stored on instrument temporarily until it is manually removed by the user. As part of the Pre-Run Checks, the instrument will confirm that there is sufficient storage space on the instrument to complete both the Sequencing Run and the configured Secondary Analyses.

If there is insufficient space to complete these tasks, the Control Software will present a warning or error to the user and require user input before proceeding. The specific messaging will vary depending on Control Software version and the amount of space that is available.

For Control Software v1.3 and above:

If there is sufficient storage space to complete the Sequencing Run but not enough space for the configured Secondary Analyses, the software will display a Warning during the Pre-Run Check indicating that there is low disk space, but the sequencing run can still proceed.

Pre-run checks warnings

There is sufficient storage space to start sequencing, but not enough space to complete onboarding secondary analysis.

If you do not clear at least XXXX GB of storage space before sequencing completes, secondary analysis will be automatically canceled and you need to manually requeue the analysis after sufficient space is made available.

The user can select Continue to proceed with the starting the Run, then perform the actions under the Delete a Run section below to clear disk space during the Run to allow the Secondary Analyses to proceed. However, if sufficient space has not been cleared before Sequencing completes, the Secondary Analysis is automatically canceled. If the Secondary Analysis is cancelled, the user the use the Requeue workflow to restart the Secondary Analysis after the Sequencing Run completes.

See Knowledge Article How to requeue or perform a new analysis of existing data on the NovaSeq X Series for additional information.

For the NovaSeq X Control Software v1.2.2 and below:

If there is insufficient data storage capacity on the Compute Engine (CE) or Single Board Computer (SBC), regardless of whether it is for sequencing run or secondary analysis, the Software displays a Pre-Run Check Error that prevents starting the Sequencing Run.

Pre-run checks errors

There is insufficient storage space to start the run.

Navigate to the Runs screen to view current runs on the instrument, and delete enough runs on the [SBC/CE] to clear at least XXXX GB of space.

Use the following steps to check the available space consumed by Runs or Resources on the instrument, then clear space by deleting completed Runs from the instrument storage. Once sufficient space has been cleared, select Retry to proceed with the Pre-Run Checks.

If the issue persists after clearing disk space by removing previous sequencing Runs or removing Resources, contact Illumina Tech Support.

Resolution Actions

Check Disk Space

1. Select the instrument icon to open the global navigation menu.

2. Select Runs.

3. The available disk space and the disk space used by runs is in the upper right-hand area.

Approximate Disk Space Utilization

Estimates are for a 300 cycle, single-sided sequencing run and will need to be doubled for a dual-sided run. Secondary analysis estimates are based on DRAGEN Germline App. Estimates vary depending on cycle number and DRAGEN Application.

Flow Cell	SBC (GB)	CE Primary (TB)	CE Secondary (TB)
1.5B	15	0.4	1
10B	19	2.1	5.5
25B	24	5.6	14.7

Delete a Run

Only delete Runs using the NovaSeq X Series Control Software and do not delete Runs through the Linux Operating System (OS). Deleting runs manually can negatively impact the control software. A deleted run cannot be requeued. Prior to deleting runs from the NovaSeq X Series Control Software, make sure the runs are backed up on a network drive or in BaseSpace Sequence Hub.

1. Select the instrument icon to open the global navigation menu.

2. Select Runs.

3. For the run to delete, select the ellipsis icon in the Action column.

4. Select one of the following options:

• Delete run data—Deletes the sequencing and analysis output folders from the instrument, but does not remove the run from the Completed tab. The run details will still be available in the control software, but the DRAGEN secondary analysis report is removed.

• Delete run—Deletes the run data and removes the run from the Completed tab.

1. In the dialog box, confirm run deletion.

2. Repeat steps 3 - 5 to delete runs as needed.

Remove Resources

Use the following instructions to remove reference genomes or reference files.

1. Select the instrument icon to open the global navigation menu.

2. Select Settings, and then select Resources.

3. Select the Genomes tab or Reference files tab.

4. For the genome or reference file to remove, select the delete icon.

5. In the dialog box, select Yes, remove to confirm.

6. Repeat steps 4 and 5 for each genome or reference file to remove. If needed, users can check the CE disk space prior to setting up a run.

If the issue persists after clearing disk space by removing previous sequencing runs, contact Illumina Tech Support.

For any feedback or questions regarding this article (Illumina Knowledge Article #7797), contact Illumina Technical Support [e-mail].