Does MiSeq verify the number of cycles in a planned run against the cycles supported by the reagent kit?

For MiSeq Control Software v3.1 and below:

The MiSeq Control Software does not cross-reference the total number of cycles programmed in the run set up compared to the number of cycles a reagent kit can support. If a run is set up with a greater number of cycles than the reagent kit supports, the MiSeq Control Software allows the run to proceed, although run performance may be impacted. Runs may stop with Best Focus or Z-motor soft focus limit errors.

For MiSeq Control Software v4.0 and above:

With the introduction of MiSeq Control Software v4.0, the Software checks the total number of cycles to ensure it is less than or equal to the total cycles supported by the loaded reagent kit. This takes into account the 7 dark cycles required for Index Read 2 if the workflow uses dual index sequencing.

If the planned cycle count exceeds the maximum number of cycles supported by the reagent kit, the control software displays the following warning message after the pre-run checks:

"Correct the Following Issues: Cycles exceed reagent kit limit"

If this error presents, review the cycle numbers for each read, and verify that the loaded kit supports the number of cycles required for the desired workflow.

For more information, refer to the following Illumina Knowledge Articles below:

How many cycles of SBS chemistry are in my kit? Maximum read length for Illumina sequencing platforms

For any feedback or questions regarding this article (Illumina Knowledge Article #3094), contact Illumina Technical Support [e-mail].