> 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/general/instrumentation-general-reference_material-list/000002287.md).

# 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.

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| *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)*.* |


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