File paths for the MiSeq

MiSeq****File Paths
There are three locations for the run folders from each run. Each location has overlapping content, though they are not mirrors of each other.
  1. 1.
    MiSeq Temp Folder: Temporary working folder for MiSeq Control Software (MCS) and Real Time Analysis (RTA) software. Contents of this folder are deleted automatically after seven days.
  2. 2.
    MiSeq Analysis Folder: As primary analysis files are generated, RTA copies files back to the Temp folder and populates the Analysis folder. When the primary analysis is complete, MiSeq Reporter (MSR) or Local Run Manager (LRM) accesses the Analysis folder to begin secondary analysis. All files written to the Analysis folder are copied to the Output folder by RTA (Windows 7 - MCS v3.1 and older) or Universal Copy Service (UCS) (Windows 10 - v4.0).
  3. 3.
    MiSeq Output Folder (or network path): RTA or UCS copies files from the Temp folder to the Output folder.
The default run folder name uses the following format:
YYMMDD_[InstrumentSerialNumber]_[Run Number]_A[FlowCellBarcode]
Run Folder Architecture\*
D:\Illumina\MiSeq Temp(or MiSeq Output or MiSeq Analysis)[Run_Folder]
  • Runinfo.xml
  • Runparameters.xml
  • InterOp folder
  • SampleSheet.csv
  • Cycle Logs:
    • D:\Illumina\MiSeq Temp[Run_Folder]\Logs
  • Thumbnail Images:
    • D:\Illumina\MiSeq Temp[Run_Folder]\Thumbnail_Images\L001\C# (folder(s) listed by cycle) (Not present in Analysis folder, but present in Temp and Output folders)
  • Offsets folder:
    • D:\Illumina\MiSeq Temp[Run_Folder]\Data\Intensities\Offsets
  • RTA Logs:
    • D:\Illumina\MiSeq Temp[Run_Folder]\Data
  • Recipes:
    • D:\Illumina\MiSeq Temp[Run_Folder]\Recipe
Analysis Files
  • bcl, stats and locs files:
    • D:\Illumina\MiSeq Analysis[Run_Folder]\Data\Intensities\BaseCalls
  • cif files:
    • D:\Illumina\MiSeq Analysis[Run_Folder]\Data\Intensities\L001\C
  • cif files (alternative location)
    • D:\Illumina\MiSeqTemp\Processed\L001\Cx.1
  • DemultiplexSummaryF1L1.txt for MiSeq Reporter
    • D:\Illumina\MiSeqAnalysis[Run_Folder]\Data\Intensities\BaseCalls\Alignment\
  • DemultiplexSummaryF1L1.txt for Local Run Manager (LRM) v2.0 and v3.0
    • D:\Illumina\MiSeqAnalysis[run folder]\Alignment_#[date and time folder]
  • FASTQ files for MiSeq Control Software (MCS) v2.5 and v2.6:
    • D:\Illumina\MiSeqAnalysis (or MiSeqOutput)[RunFolderName]\Data\Intensities\BaseCalls
  • FASTQ files for MCS v3.1/LRM v2.0 and MCS v4.0/LRM v3.0
    • D:\Illumina\MiSeqAnalysis (or MiSeqOutput)[RunFolderName]\Alignment_1[autogenerated folder with date and time when analysis started]\Fastq
  • MCS v3.1 and older LRM Analysis Logs: D:\Illumina\MiSeqAnalysis[RunFolderName]\Alignment_#[date_time]
Maintenance Logs
D:\Illumina Maintenance Logs (available files inside the folder):
  • Green LED Log.csv
  • Red LED Log.csv
  • Temperature Log Chiller.csv
  • Temperature Log Flow cell #1.csv
  • WashLog.xml
Other important files
  • MCS Logs
    • D:\Illumina\MiSeqControlSoftware
  • MiSeqSoftware.Options.cfg file:
    • Windows 7: D:\Illumina\MiSeqControlSoftware
    • Windows 10: C:\ProgramData\Illumina\MiSeqControlSoftware
  • System check results:
    • D:\DiagResults[Folder titled with the date the check is performed]
  • Wash log:
    • D:\Illumina Maintenance Logs
  • WashStatus.xml file:
    • MCS v3.1 and v2.6: - D:\ root directory
    • MCS v4.0: - C:\ProgramData\Illumina\MiSeq Control Software
  • Cloud API key:
    • Windows 7: C:\MiSeq Config
    • Windows 10: C:\ProgramData\Illumina\MiSeqSoftware
  • BaseSpace Broker folder:
    • D:\Illumina\basespacebroker
  • MiSeqOverride.cfg
    • Windows 7: C:\MiSeq Config
    • Windows 10: C:\ProgramData\Illumina\MiSeq
  • Runcompletionstatus.xml
    • D:\Illumina\MiSeqOutput[Run_Folder]
MiSeq Control Software v4 specific file paths
  • UCS Logs and Run folders
    • C:\ProgramData\Illumina\UniversalCopyService
  • LRM Logs folder
    • C:\ProgramData\Illumina\LocalRunManager
Additional Resources: \*For an in-depth description of each folder/function, review the MiSeq Run Folder Quick Reference Card (MCS v2.6 and older).
For any feedback or questions regarding this article (Illumina Knowledge Article #1678), contact Illumina Technical Support [email protected].
Last modified 23d ago
© 2023 Illumina, Inc. All rights reserved. All trademarks are the property of Illumina, Inc. or their respective owners. Trademark information: Privacy policy: