> 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-i100-series/instrumentation-miseq-i100-series-reference_material-list/000009212.md).

# File paths on the MiSeq i100 Series

**Background**

The MiSeq i100 Series instrument operates in Kiosk mode and the underlying Linux Operating System (OS) and file system directories are not available to the user. The following directories outline the file paths for the Run Output directory that is copied from the instrument to the Default Output folder for the configured External Storage.

**Run Output Directory**

* //\[server]/\[share]/\[output-directory]/\[RunId]/
  * Analysis/\[#]/Data/ where # is the analysis number.\
    \- ../\[Dragen App]/ora\_fastq/ : FASTQ Files (DRAGEN/ORA)\
    \- ../\[Dragen App]/fastq/ : FASTQ Files (GZIP):\
    \- ../Demux/ : Demultiplex\_Stats.csv, Top\_Unknown\_Barcodes.csv, IndexMetricsOut.bin
  * Config/
  * CopyComplete.txt
  * Data/\
    \- BaseCall Files: ../Intensities/BaseCalls/L001/C\[#].1/L001\_1.cbcl where # is the cycle number.
  * FirmwareInformation.xml
  * InstrumentAnalyticsLogs/
  * InterOp/
  * Logs/
  * Manifest.tsv
  * RTAComplete.txt
  * RTAExited.txt
  * RunCompletionStatus.xml
  * RunInfo.xml
  * RunParameters.xml
  * SampleSheet.csv

For each on-instrument Analysis, there is an additional **CopyComplete.txt** flag file generated in the output directory within the numbered Analysis folder (e.g. //server/share/\[output-directory]/\[InstrumentRunId]/Analysis/\[#]/) that signals completion of Analysis file copy.

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #9212), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009212%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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