# 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](https://knowledge.illumina.com/instrumentation/novaseq-6000/instrumentation-novaseq-6000-troubleshooting-list/000003046/?utm_source=agent\&utm_medium=email\&utm_campaign=kb)
* 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.

  ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-52d15c3dd260e68671ea8a93d6e160d4828a6e3b%2Fimage1.png?alt=media\&token=ba4c45ad-2844-4b81-8048-e3bc25c086fc)

**Troubleshooting steps:**

1. 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](https://www.illumina.com/company/contact-us.html#/united-states/technical-support) for the next steps.

2. 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](https://www.illumina.com/company/contact-us.html#/united-states/technical-support).
  * If pressure is still outside the expected range, contact Illumina Technical Support (<techsupport@illumina.com>) with a screenshot of the results.

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #1309), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001309%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |