# File paths for the NextSeq 500/550

The run folders on the NextSeq 500/550 include run data, along with many files that are helpful for reviewing run performance and troubleshooting, if necessary.

**NextSeq Control Software (NCS) 2.2.x and 4.0.x Run Folder:**\
The file path of each run folder is:

* D:\Illumina\NextSeq Control Software Temp\[Run\_Folder]

Key files in this location include:

* Runinfo.xml
* Runparameters.xml
* InterOp folder
* Thumbnail Images
* SampleSheet.csv
* Cycle Logs:
  * (D:\Illumina\ NextSeq Control Software Temp \[Run\_Folder]\Logs)
* Diagnostic.00.log:
  * (D:\Illumina\ NextSeq Control Software Temp \[Run\_Folder]\Logs)
* Focus Images:
  * (D:\Illumina\ NextSeq Control Software Temp\[Run\_Folder]\Images\Focus\L00X\C1.1)
* RTA Logs:
  * (D:\Illumina\ NextSeq Control Software Temp\[Run\_Folder]\RTALogs)
* RTA Config:
  * (D:\Illumina\ NextSeq Control Software Temp\[Run\_Folder]\Data\Intensities\RTAConfiguration.xml)
* FirmwareVersions.txt:
  * (D:\Illumina\ NextSeq Control Software Temp\[Run\_Folder]\Config)
* DemultiplexSummaryF1L1.txt
  * (Generated after FASTQ generation completes): \[run folder]\Alignment\_#\[date and time folder]

**Analysis Files**

BCL Files (raw data output from sequencing) are saved in 2 locations:

* D:\Illumina\NextSeq Control Software Temp\[Run Folder]\Data\Intensities\Basecalls
* \[Output Folder]\[Run Folder]\Data\Intensities\Basecalls

FASTQ files for local LRM GenerateFASTQ analysis

* D:\Illumina\NextSeq Control Software Temp\[Run ID]\Alignment\_#\[Date and Time]\Fastq

**Additional helpful file paths:**

* NCS Logs in Windows 7: (C:\Illumina\NextSeq Control Software\Logs)
* NCS Logs in Windows 10: (D:\Illumina\NextSeq Control Software\Logs)
* Maintenance Logs: (D:\Illumina Maintenance Logs)
* Preventative Maintenance (PM): D:\Illumina\PreventativeMaintenance
* NextSeq Control Software Config: (C:\ProgramData\Illumina\NextSeq Control Software\InstrumentShell.NextSeqControlSoftware.Options.cfg)
* BaseSpace Broker Logs: D:\Illumina\BaseSpace broker (NCS 2.2.x only)
* Restart Universal Copy Service (UCS): (C:\ProgramFiles\Illumina\UniversalCopyService\ucs.exe) (NCS 4.0.x only)
* System Check Results (all): D:\Illumina\SystemCheckResults

**Beadarray folder:**\
(The NextSeq 550 can be used to scan select beadarrays.)

* \[Date]\_\[Instrument Name]\_\[Scan#]\_\[Barcode]\[Barcode]\Config folder
* \[Date]\_\[Instrument Name]\_\[Scan#]\_\[Barcode]\[Barcode]\Focus folder
* \[Date]\_\[Instrument Name]\_\[Scan#]\_\[Barcode]\[Barcode]\Logs folder
* \[Date]\_\[Instrument Name]\_\[Scan#]\_\[Barcode]\[Barcode]\GTC files
* \[Date]\_\[Instrument Name]\_\[Scan#]\_\[Barcode]\[Barcode]\IDAT files
* \[Date]\_\[Instrument Name]\_\[Scan#]\_\[Barcode]\[Barcode]\Image files
* \[Date]\_\[Instrument Name]\_\[Scan#]\_\[Barcode]\[Barcode]\[Barcode]\_sample\_metrics.csv
* \[Date]\_\[Instrument Name]\_\[Scan#]\_\[Barcode]\[Barcode]\[Barcode]\_section\_metrics.csv
* \[Date]\_\[Instrument Name]\_\[Scan#]\_\[Barcode]\ScanrParameters.xml

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                        |
| :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #2072), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002072%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


---

# Agent Instructions: 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:

```
GET https://knowledge.illumina.com/instrumentation/nextseq-500-550/instrumentation-nextseq-500-550-reference_material-list/000002072.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
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.