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

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