# File Paths on the iSeq 100

**iSeq 100 File Paths:**

**Temporary Run Folder:** D:\Illumina\iSeq Runs\[RunFolder]

* Data
  * \Intensities\Basecalls\L001 (to locate BCL files)
* InterOp
* Logs
  * Cycles
* RTALogs
* Thumbnail\_Images
  * \L001\Cx.1 (where "x" corresponds to cycle number)
* RunCompletionStatus.xml
* RunInfo.xml
* RunParameters.xml
* SampleSheet.csv

**Default Output Run Folder**\*\*:\*\* D:\SequencingRuns\[RunFolder]

* Data
  * \Intensities\Basecalls\L001 (to locate BCL files)
* InterOp
  * IndexMetricsOut.bin
* Logs
  * Logs.zip
* RTALogs
* Thumbnail\_Images
  * \L001\Cx.1 (where "x" corresponds to cycle number)
  * \NormalizedFC for a zoomed-out picture of flow cell (useful in certain troubleshooting instances)
* RunCompletionStatus.xml
* RunInfo.xml
* RunParameters.xml
* SampleSheet.csv

**Secondary Analysis Files:** D:\Illumina\SequencingRuns\[Runfolder]\Alignment\_1 where "alignment\_#" is the number of the analysis/requeue, such as "1" for the initial analysis

* Present when Local Run Manager performed secondary analysis.
* DemultiplexSummaryF1L1.txt
* SampleSheetUsed.csv

**Pre-Run Check Logs**\*\*:\*\* D:\Illumina\iSeq Pre-Run Checks

* Images
* Logs
* Reports

**System Check Results**\*\*:\*\* D:\Illumina\iSeq System Checks\[Date System Check performed]

**Control Software Logs**\*\*:\*\* C:\Program Files\Illumina\iSeqSbsControlSoftwareServer\Logs

**Universal Copy Service (UCS) Logs**\*\*:\*\* C:\ProgramData\*\Illumina\UniversalCopyService\Logs\
\*The ProgramData folder may be hidden. To un-hide files, click on the View tab in the File Explorer window and ensure the box for “Hidden items” is checked.

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                        |
| :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #2287), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002287%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/general/instrumentation-general-reference_material-list/000002287.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.