# File paths on the NovaSeq X Series

**Control Software Logs**

* /usr/local/illumina/logs/novaseq-x-series-control-software

**Temporary Run Folders (SBC):**

* Pre-Run Check Files:
  * /usr/local/illumina/runs/setup-A or ../setup-B
* Run folder on control computer:
  * /usr/local/illumina/runs/\[RunID]/\
    \- Config/\
    \- InstrumentAnalyticsLogs/\
    \* .imf Files\
    \- Logs.zip/\
    \* LowLevelDiagnostics\
    \* AutoCenterLineScan\
    \* Cycles\
    \* run-setup\
    \* AdvancedFocusModelGeneration\
    \* AutoDetilt\
    \* Config\
    \* FindSurface\
    \* FlowCellThickness\
    \* ITF\
    \* FwLogs\
    \* \*\_PostRun.log\
    \- RunParameters.xml

**Run folder on Compute Engine (CE):**

* /usr/local/illumina/mnt/runs/\[RunID]/
  * Analysis/#/ (if onboard analysis has been performed)
  * Data/Intensities/BaseCalls/L001/Cx.1/, where x is the cycle number.\
    \- L001\_1.cbcl\
    \- L001\_2.cbcl
  * InterOp/
  * Thumbnail\_Images/L00X/, where X is the Lane number
  * RTA.cfg
  * RTAComplete.txt
  * RTAExited.txt
  * RunInfo.xml
  * SampleSheet.csv

**Secondary Analysis Files** (present when local DRAGEN secondary analysis has been performed):

* Local FASTQ Files (DRAGEN / ORA Compression)
  * /usr/local/illumina/mnt/runs/\[RunID]/Analysis/\[#]/Data/\[DRAGEN App]/ora\_fastq\
    \- Where # is the number of the analysis/requeue, such as "1" for the initial analysis and \[DRAGEN App] is the Application uses, such as `BCLConvert`.
* Local FASTQ Files (GZIP)
  * /usr/local/illumina/mnt/runs/\[RunID]/Analysis/\[#]/Data/\[DRAGEN App]/fastq\
    \- Where # is the number of the analysis/requeue, such as "1" for the initial analysis and \[DRAGEN App] is the Application uses, such as `BCLConvert`.
* Demultiplexing Reports and IndexMetricOut.bin file
  * /usr/local/illumina/mnt/runs/\[RunID]/Analysis/\[#]/Data/Demux\
    \- IndexMetricsOut.bin\
    \- Demultiplex\_Stats.csv\
    \- Index\_Hopping\_Counts.csv\
    \- Top\_Unknown\_Barcodes.csv\
    \- AggregatedReports (html report containing Demux stats)
* Folder on network output directory
  * //server/share/\[output-directory]/\[RunID]/Analysis/\[#]/Data

**FASTQ files Notes:**

If FASTQ files were saved, they are found in the folder specific to the workflow the sample was analyzed with. For example:

* For DRAGEN FASTQ Generation only samples, the sample FASTQ files are found in the BCLConvert folder.
* For DRAGEN Enrichment samples, the sample FASTQ files are found in the DragenEnrichment folder.

**Output directory** Combined contents from partial run folders on control computer and CE:

* //server/share/\[output-directory]/\[RunID]/
  * Analysis/#/Data
  * CopyComplete.txt
  * Data/Intensities/BaseCalls/L001/Cx.1/\
    \- L001\_1.cbcl\
    \- L001\_2.cbcl
  * InstrumentAnalyticsLogs/
  * InterOp/
  * Logs/
  * RTA.cfg
  * RTAComplete.txt
  * RunCompletionStatus.xml
  * RunInfo.xml
  * RunParameters.xml
  * SampleSheet.csv

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