Comment on page

Troubleshooting Sample Sheet will not Load into MiSeq Control Software

These errors are usually seen when the MiSeq Control Software (MCS) cannot find the sample sheet for the run or the sample sheet is formatted incorrectly. This may be resolved by renaming or moving the sample sheet to a new location.
Sample Sheet errors may also occur during Pre-run checks. Examples of errors include:
  • An error has occured while reading in the recipe fragments.
  • Chemistry step ' firstReadPreparation' is invalid: Error in PumpToFlowCell Node. Could not find either a reagent name or a solution.
These errors also require reformatting/editing the sample sheet. Troubleshooting steps:
Check Sample sheet file location:
  • The sample sheet must be located in the SampleSheets folder.
    • The default sample sheet location is D:\Illumina\MiSeq Control Software\SampleSheets.
    • This can be changed in the Folder Settings tab of Run Options, or specified for a particular run.
    • If the sample sheet is not in this folder, make a copy and place it in the specified folder.
  • Browse directly to a sample sheet if desired.
Check Sample sheet format:
  • The best way to ensure correct formatting is to generate the sample sheet in Local Run Manager (LRM) or Illumina Experiment Manager (IEM). If these software are not used, the sample sheet must be created as a comma-separated text file according to the format described in the MiSeq Sample Sheet Quick Reference Guide. The file name is typically the same as the serial number from the reagent cartridge, although this is not required. The extension must be .csv.
  • There are several illegal characters that should not be used in a sample sheet or title, including:
    ? ( ) [ ] / \ = + < > : ; " ' , * ^ | &
These characters can prevent the sample sheet from being loaded correctly.
For any feedback or questions regarding this article (Illumina Knowledge Article #1455), contact Illumina Technical Support [email protected].
Last modified 2mo ago
© 2023 Illumina, Inc. All rights reserved. All trademarks are the property of Illumina, Inc. or their respective owners. Trademark information: Privacy policy: