# 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."
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)*.* |
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