> 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-1000-2000/instrumentation-nextseq-1000-2000-reference_material-list/000002443.md).

# File paths on the NextSeq 1000/2000

The NextSeq 1000/2000 saves each run folder to a temporary run folder and a networked output folder. The networked output folder is optional if the run is sent to BaseSpace Sequence Hub (BSSH) with the Run Monitoring and Storage option. The run folder location(s) and an overview of the contents are listed below. This file path list is not exhaustive.

**Temporary Run Folder**: /usr/local/Illumina/runs/\[runfolder]

* Run Performance Files:
  * Autocenter
  * Autofocus
  * Config
  * Data/Intensities/BaseCalls/L001/Cx.1
    * L001\_1.cbcl
    * L001\_2.cbcl
  * Data/Intensities/BaseCalls/s\_\[lane]\_\[tile].filter
    * Filter files, available after cycle 26, for specifying calls that passed filter
  * Data/Intensities/s\_\[lane].locs
    * Cluster Location Files, specifies XY coordinates of each cluster in a tile
  * FocusModelGeneration
    * Cycle 1, etc.
  * InterOp
  * Logs
    * Cycles
      * Firmware
    * Logs.zip: contains all contents of the Logs folder but is zipped for easy transfer
  * Recipe
    * EffectiveRecipe.xml (recipe used)
  * RunCompletionStatus.xml
  * RunInfo.xml
  * RunParameters.xml
  * SampleSheet.csv

**Secondary Analysis Files:** Present when local DRAGEN performed secondary analysis.

* \[run folder]/Analysis/\[analysis #]/Data/Reports/ where "analysis #" is the number of the analysis/requeue, such as "1" for the initial analysis
  * Demultiplex\_Stats.csv
  * Top\_Unknown\_Barcodes.csv
  * IndexMetricsOut.bin
  * SampleSheet.csv

**Output Folder**: contents mirror the Temporary Run Folder.

Table 1: Flag Files for the NextSeq 1000/2000 Integrated Software Processes. Flag files are created when select processes are complete.

<table data-header-hidden><thead><tr><th valign="top"></th><th valign="top"></th><th valign="top"></th><th valign="top"></th></tr></thead><tbody><tr><td valign="top">File Name</td><td valign="top">Process File is Flagging</td><td valign="top">Present in Temporary Run Folder</td><td valign="top">Present in Output Run Folder</td></tr><tr><td valign="top">RunCompletionStatus.xml</td><td valign="top">Primary Sequencing complete</td><td valign="top">Yes</td><td valign="top">Yes</td></tr><tr><td valign="top">RTAComplete.txt</td><td valign="top">Real Time Analysis (RTA3) complete</td><td valign="top">Yes</td><td valign="top">Yes</td></tr><tr><td valign="top">CopyComplete.txt</td><td valign="top">Universal Copy Service transfer complete</td><td valign="top">No</td><td valign="top">Yes</td></tr></tbody></table>

**System check results:** /usr/local/illumina/system-checks\
**Recipe folder**: /usr/local/illumina/recipes\
**Networking fstab**: /etc/fstab

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #2443), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002443%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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