> 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-ruo/instrumentation-miseq-ruo-troubleshooting-list/000001455.md).

# Troubleshooting Sample Sheet will not Load into MiSeq Control Software

**Background**

Errors when loading a Sample Sheet in the MiSeq Control Software (MCS) can be caused by:

* MCS unable to find the sample sheet for the run
* The sample sheet is formatted incorrectly

Sample Sheet errors may also occur during Pre-run checks. Examples of errors include:

* *An error has occurred 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.*

**Troubleshooting**

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) (MiSeq Control Software v3.1 or later) or Illumina Experiment Manager (IEM) (MiSeq Control Software v2.6.2 or earlier). If these software are not used, the sample sheet must be created as a comma-separated text file (\*.csv) according to the format described in the [MiSeq Sample Sheet Quick Reference Guide](https://emea.support.illumina.com/downloads/miseq_sample_sheet_quick_reference_guide_15028392.html?langsel=/de/). The file name is typically the same as the serial number from the reagent cartridge, although this is not required.
* The file extension must be **.csv**
* There are several illegal characters that should not be used in a sample sheet or title, including:

**? ( ) \[ ] / \ = + < > : ; " ' , \* ^ | &**

These characters prevent the sample sheet from being loaded correctly.

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                        |
| :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #1455), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001455%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter:

```
GET https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000001455.md?ask=<question>&goal=<endgoal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.