> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000001432.md).

# Troubleshooting 'Index outside the bounds of the array' error on the MiSeq

This error generally occurs when the MiSeq Software is unable to calculate the focus model for one or more surfaces on the flow cell.

This issue can be caused by several potential root causes, including:

* Low signal intensity due to underclustering.
* Poor signal-to-noise ratio due to overclustering.
* Issues with library design or custom sequencing primers.
* Issues with the flow cell consumable that prevents normal focus model calculation.

**Troubleshooting steps:**

1. Check the library loading concentration to determine if libraries may be under or overclustered. If optimization is needed, the following article provides best practices: [How to achieve more consistent cluster density on Illumina sequencing platforms](/instrumentation/general/instrumentation-general-reference_material-list/000001481.md).
2. Perform the instrument system checks using the flow cell from the sequencing run as described in [How to perform a System Check on the MiSeq](/instrumentation/miseq/instrumentation-miseq-reference_material-list/000001777.md).
3. If the system check passes, proceed with setting up a repeat sequencing run.
4. If there is a failure in any of the system checks or the following run stops at cycle 1 due to another error, contact [Illumina Technical Support](https://www.illumina.com/company/contact-us.html#/united-states/technical-support) (<techsupport@illumina.com>) for further assistance.

**Additional Resources:**

* [Denature and Dilute Libraries for the MiSeq system](https://support-docs.illumina.com/IN/MiSeq_DnD/Content/MiSeq/DnD-MiSeq.htm?protocol=ampliseq)
* [MiSeq System Custom Primers Guide](https://support.illumina.com/downloads/miseq-system-custom-primers-guide-15041638.html)

**For futher related issues, see the Knowledge Article:**

* [Troubleshooting cycle 1 errors on the MiSeq](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000001430.md)

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #1432), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001432%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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