File Paths on the iSeq 100

iSeq 100 File Paths:

Temporary Run Folder: D:\Illumina\iSeq Runs[RunFolder]

• Data

  • \Intensities\Basecalls\L001 (to locate BCL files)

• InterOp

• Logs

  • Cycles

• RTALogs

• Thumbnail_Images

  • \L001\Cx.1 (where "x" corresponds to cycle number)

• RunCompletionStatus.xml

• RunInfo.xml

• RunParameters.xml

• SampleSheet.csv

Default Output Run Folder**:** D:\SequencingRuns[RunFolder]

• Data

  • \Intensities\Basecalls\L001 (to locate BCL files)

• InterOp

  • IndexMetricsOut.bin

• Logs

  • Logs.zip

• RTALogs

• Thumbnail_Images

  • \L001\Cx.1 (where "x" corresponds to cycle number)

  • \NormalizedFC for a zoomed-out picture of flow cell (useful in certain troubleshooting instances)

• RunCompletionStatus.xml

• RunInfo.xml

• RunParameters.xml

• SampleSheet.csv

Secondary Analysis Files: D:\Illumina\SequencingRuns[Runfolder]\Alignment_1 where "alignment_#" is the number of the analysis/requeue, such as "1" for the initial analysis

• Present when Local Run Manager performed secondary analysis.

• DemultiplexSummaryF1L1.txt

• SampleSheetUsed.csv

Pre-Run Check Logs**:** D:\Illumina\iSeq Pre-Run Checks

• Images

• Logs

• Reports

System Check Results**:** D:\Illumina\iSeq System Checks[Date System Check performed]

Control Software Logs**:** C:\Program Files\Illumina\iSeqSbsControlSoftwareServer\Logs

Universal Copy Service (UCS) Logs**:** C:\ProgramData*\Illumina\UniversalCopyService\Logs *The ProgramData folder may be hidden. To un-hide files, click on the View tab in the File Explorer window and ensure the box for “Hidden items” is checked.

For any feedback or questions regarding this article (Illumina Knowledge Article #2287), contact Illumina Technical Support [e-mail].