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. Insufficient data storage capacity on the Compute Engine (CE) or Single Board Computer (SBC) can lead to delays in starting sequencing runs with a warning notification occurring during the pre-run check.

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 to check the available space consumed by Runs or Resources on the instrument, then clear space by deleting completed Runs from the instrument storage.

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

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].