Links

File paths on the NovaSeq X/X Plus

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
    • 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
    • /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 [email protected].
Last modified 11d ago
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