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 over loading (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 over or under loaded.

2. Perform the instrument system checks using the flow cell from the sequencing run as described in the MiSeq System Guide.

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, email Illumina Technical Support at [e-mail] for further assistance.

Additional Resources:

• MiSeq System Denature and Dilute Libraries Guide

• MiSeq System Custom Primers Guide

For further information, search for Knowledge Base articles:

• How to achieve more consistent cluster density on Illumina sequencing platforms

• System checks for Illumina sequencing platforms

• Best Focus and No Usable Signal errors on the MiSeq

For any feedback or questions regarding this article (Illumina Knowledge Article #1432), contact Illumina Technical Support [e-mail].