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Troubleshooting MiSeq "a valid index kit must be provided for the selected library prep kit" error
This error may be seen with a MiSeq running MiSeq Control software (MCS) v4 with Local Run Manager (LRM) v3. Because (Instrument Experiment Manager) IEM and LRM v3 format information differently, IEM sample sheets are not compatible with LRM v3 and cannot be converted to LRM v3 sample sheets.
Importing an IEM sample sheet into LRM v3 during the new run setup will trigger the error message “a valid index kit must be provided for the selected library prep kit”.
Download the template sample sheet from the desired LRM module, as described in “How to find sample sheet templates for MCS v4.0 LRM modules” article, manually populate it, and upload it back into the module while setting up a new run in LRM v3 or directly input run information into LRM v3 module new run setup without using the Import Sample Sheet function.