Troubleshooting vacuum failures and flow cell vacuum is no longer engaged message on NovaSeq 6000
Vacuum issues can happen at the start of a run or during a run, and have different underlying causes.
Vacuum issues at the start of the run
If there are vacuum issues when loading a flow cell, please see this article: How to troubleshoot flow cell clamp or vacuum is unable to engage errors when loading flow cells on the NovaSeq 6000
If the flow cell loads, a vacuum failure may present as a clustering failure due to the inability to flow through the flow cell.
Phenotype of runs with vacuum issues
These manifest as low intensity and low Q30 at the inlet of the flow cell (pictured below).
This is caused by flow cell quality issues or glass shards at the bottom of the flow cell.
Glass shards on the flow cell stage may also impact flow cell vacuum engagement.
Troubleshooting steps:
Inspect flow cell glass and flow cell stage.
If no glass shards are present, clean flow cell and flow cell stage with an alcohol wipe and a dry, lint-free wipe to remove any debris on these surfaces.
For more information on how to clean the flow cell and flow cell stage, search for Knowledge Base article Troubleshooting NovaSeq 6000 flow cell loading issues video.
Check for reagent leakage on or around the flow cell holder.
If leaking is observed, contact Illumina Tech Support for the next steps.
Check the flow cell vacuum pressure (PSI) in NovaSeq Service Software (NVSS).
Close the NovaSeq Control Software and launch NovaSeq Service Software (NVSS).
Once initialized, select the Flow Cell option on the main screen.
Load wash flow cells on Sides A and B.
Pressure readings for wash flow cells are around -90 kPa and show a steady green check mark for the sensor.
If pressure is low or the sensor is not steady, clean the flow cell and stage one more time (with alcohol and a lint-free wipe) and re-check pressure values.
If vacuum pressure is within the expected range, perform a power cycle on the instrument and proceed with the next run. - For more information on how to power cycle the instrument, search for Knowledge Base article How to Power Cycle the NovaSeq 6000 System? - If the issue reoccurs on the next run, contact Illumina Technical Support.
If pressure is still outside the expected range, contact Illumina Technical Support (techsupport@illumina.com) with a screenshot of the results.
For any feedback or questions regarding this article (Illumina Knowledge Article #1309), contact Illumina Technical Support techsupport@illumina.com. |
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