File paths on the MiSeq i100 Series

Background

The MiSeq i100 Series instrument operates in Kiosk mode and the underlaying Linux Operating System (OS) and file system directories will not be available to the user. The following directories outline the file paths for the Run Output directory that is copied from the instrument to the Default Output folder for the configured External Storage.

Run Output Directory

• //server/share/[output-directory]/[InstrumentRunId]/

  • Analysis/[#]/Data/ where # is the analysis number. - FASTQ Files (DRAGEN/ORA): ./[Dragen App]/ora_fastq/ - FASTQ Files (GZIP): ./[Dragen App]/fastq/ - Demultiplexing Reports and IndexMetricOut.bin: ./Demux/

  • Config/

  • CopyComplete.txt

  • Data/ - BaseCall Files: ./Intensities/BaseCalls/L001/C[#].1/L001_1.cbcl where # is the cycle number.

  • FirmwareInformation.xml

  • InstrumentAnalyticsLogs/

  • InterOp/

  • Logs/

  • Manifest.tsv

  • RTAComplete.txt

  • RTAExited.txt

  • RunCompletionStatus.xml

  • RunInfo.xml

  • RunParameters.xml

  • SampleSheet.csv

For each on-instrument Analysis, there is an additional CopyComplete.txt flag file generated in the output directory within the numbered Analysis folder (e.g. //server/share/[output-directory]/[InstrumentRunId]/Analysis/[#]/): Signals completion of Analysis file copy.

For any feedback or questions regarding this article (Illumina Knowledge Article #9212), contact Illumina Technical Support [e-mail].