> 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/nextseq-500-550/instrumentation-nextseq-500-550-troubleshooting-list/000005028.md).

# Troubleshooting an empty output folder on the NextSeq 500/550 NCS 4.0

Windows 10 on NextSeq 500/550 systems upgraded to NextSeq Control Software (NCS) v4.0+ have additional requirements for connectivity to network shares. If system is not set up properly, sequencing runs may complete without errors and all data available in Temp folder, but no data available in the output folder.

**Background:**

* Can happen with local (D:\ or external USB drive) or networked server.
* Run completes without errors displayed in NCS.
* It is independent of chosen run mode set up (Local Run Manager (LRM) or Manual.
* Full run data generated in local Temp run folder (D:\Illumina\NextSeq Control Software Temp)

**Troubleshooting steps:**

* Manually transfer run data files from original Temp folder (D:\Illumina\NextSeq Control Software Temp\[Run ID]) to the output directory.
* Ensure the system is set with correct folder depth rules
  * //\[server]/folder1/
  * //\[server]/folder1/folder2
  * D:\[folder1]\[folder2]
* In case the system is not connect to the internet, disable the following setting under NextSeq Control Software > System Settings
  * "Send Instrument Performance Data to Illumina"
* If subsequent runs are still not transferred, follow the guidance on Knowledge Article **Troubleshooting Universal Copy Server error on the NextSeq 500/550 (NCS 4.0+)**.
* If issue persists, contact [Illumina Technical Support](https://www.illumina.com/company/contact-us.html#/united-states/technical-support) for further assistance.

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                        |
| :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #5028), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000005028%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/nextseq-500-550/instrumentation-nextseq-500-550-troubleshooting-list/000005028.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.