How to troubleshoot errors during the pre run Wet Checks on the NovaSeq X/X Plus

Background

The Pre-Run Checks are a series of tests that help ensure the instrument is ready to perform a sequencing run. They consist of Software, Dry, and Wet Check stages. The Wet Checks will pierce the buffer cartridge and flow buffer through the flow cell to confirm that the fluidics circuit is performing as expected.

If the instrument is unable to verify the fluidics circuit is working as expected, the Control Software will present a notification indicating the Wet Checks were unsuccessful.

Recovering the Reagent Cartridge

If a dual-sided run was setup and the Pre-Run Checks were unsuccessful on only one side, see the following steps to recover the Reagent Cartridge with the Lyo Insert and Library Strip tube from the affected Side.

1. On the Pre-Run Checks screen, select Cancel Side [A/B] to cancel the affected run and allow the other Side to proceed.

2. Fill ALL wells of a Wash Reagent Cartridge with DI water.

3. Once the Run has started on the successful side, select the the instrument icon, then select Settings, then select Unlock Doors.

4. From the Unlock Doors user interface (UI), select the checkbox for the affected Side and then select Unlock.

   1. The side currently sequencing will be greyed out and cannot be selected.

5. Once the door is open, remove the Reagent Cartridge then load the filled Wash Reagent Cartridge on the affected side.

   1. The Reagent Cartridge can be transferred to another NovaSeq X Series instrument for immediate use, stored at 4° C for up to 72 hours, or re-frozen once at -20° C for longer term storage.

6. Leave the spent Buffer Cartridge in place on the affected side.

7. Close the reagent drawer and the instrument door, then select Lock Doors.

8. Once the Run completes on the successful side, see the Troubleshooting Actions below.

Troubleshooting Actions

If this issue presents during the Pre-Run Checks, collect the following information and files from the instrument:

1. Remove the flow cell and visually confirm if flow cell lanes appear wet or dry

2. Inspect the flow cell gasket and the instrument flow cell holder/manifold for any liquid or precipitate

3. Collect the run setup logs from the following directory based on the instrument side that presented the error from the following directory(ies):

   1. /usr/local/illumina/runs/setup-A or ../setup-B

Once this information is collected, contact Illumina Tech Support for further assistance.

For any feedback or questions regarding this article (Illumina Knowledge Article #7951), contact Illumina Technical Support [email protected].