File paths on the NextSeq 1000/2000

The NextSeq 1000/2000 saves each run folder to a temporary run folder and a networked output folder. The networked output folder is optional if the run is sent to BaseSpace Sequence Hub (BSSH) with the Run Monitoring and Storage option. The run folder location(s) and an overview of the contents are listed below. This file path list is not exhaustive.

Temporary Run Folder: /usr/local/Illumina/runs/[runfolder]

• Run Performance Files:

  • Autocenter

  • Autofocus

  • Config

  • Data/Intensities/BaseCalls/L001/Cx.1 - L001_1.cbcl - L001_2.cbcl

  • FocusModelGeneration - Cycle 1, etc.

  • InterOp

  • Logs - Cycles * Firmware - Logs.zip: contains all contents of the Logs folder but is zipped for easy transfer

  • Recipe - EffectiveRecipe.xml (recipe used)

  • RunCompletionStatus.xml

  • RunInfo.xml

  • RunParameters.xml

  • SampleSheet.csv

Secondary Analysis Files: Present when local DRAGEN performed secondary analysis.

• [run folder]/Analysis/[analysis #]/Data/Reports/ where "analysis #" is the number of the analysis/requeue, such as "1" for the initial analysis

  • Demultiplex_Stats.csv

  • Top_Unknown_Barcodes.csv

  • IndexMetricsOut.bin

  • SampleSheet.csv

Output Folder: contents mirror the Temporary Run Folder.

Table 1: Flag Files for the NextSeq 1000/2000 Integrated Software Processes. Flag files are created when select processes are complete.

File Name	Process File is Flagging	Present in Temporary Run Folder	Present in Output Run Folder
RunCompletionStatus.xml	Primary Sequencing complete	Yes	Yes
RTAComplete.txt	Real Time Analysis (RTA3) complete	Yes	Yes
CopyComplete.txt	Universal Copy Service transfer complete	No	Yes

System check results: /usr/local/illumina/system-checks

Recipe folder: /usr/local/illumina/recipes

Networking fstab: /etc/fstab

For any feedback or questions regarding this article (Illumina Knowledge Article #2443), contact Illumina Technical Support [e-mail].