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 - 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/BCLConvert/ora_fastq - Where # is the number of the analysis/requeue, such as "1" for the initial analysis

• Local FASTQ Files (GZIP)

  • /usr/local/illumina/mnt/runs/[RunID]/Analysis/[#]/Data/BCLConvert/fastq - Where # is the number of the analysis/requeue, such as "1" for the initial analysis

• Demultiplexing Reports and IndexMetricOut.bin file

  • /usr/local/illumina/mnt/runs/[RunID]/Analysis/[#]/Data/Demux

• Folder on network output directory

  • //server/share/[output-directory]/[RunID]/Analysis/[#]/Data

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

  • CopyComplete.txt

For any feedback or questions regarding this article (Illumina Knowledge Article #7515), contact Illumina Technical Support [e-mail].