# Pre Run check failed with an alignment check failure on the NextSeq 1000/2000

Error notification in Control Software: "An alignment check failed. Reload the flow cell and retry the pre-run check. If the problem persists, contact Illumina Technical Support."

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-9d7af984e4d68ab8de079b0a08238406b35a3357%2Fimage1.jpg?alt=media\&token=a129e0ae-2388-4248-8f0a-3dffcc00964d)

If this error occurs during the dry pre-run checks, the consumables are **not** marked as used.

**Troubleshooting steps**:

* If this error occurs, reseat the flow cell and repeat the pre-run checks.
* If error persists, power cycle the instrument [How to power cycle the NextSeq 1000/2000](https://knowledge.illumina.com/instrumentation/nextseq-1000-2000/instrumentation-nextseq-1000-2000-reference_material-list/000003038)
* If error persists, attempt pre-run checks with a different flow cell.
  * If resolved by a new flow cell, the flow cell quality is the suspected root cause. Provide the lot and serial number to [Illumina Technical Support](https://www.illumina.com/company/contact-us.html#/united-states/technical-support) for replacement.
* If error persists with alternate flow cell, collect the following Logs and contact [Illumina Technical Support](https://www.illumina.com/company/contact-us.html#/united-states/technical-support) for file transfer link and next steps:
  * NextSeq 1000/2000 control software logs: /usr/local/Illumina/logs/nextseq1k2k-control-software
  * Pre-run check logs: usr/local/Illumina/Runs/Setup/\[Date\_Time]

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #3529), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000003529%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |