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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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