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.
System check results: /usr/local/illumina/system-checks
Recipe folder: /usr/local/illumina/recipes
Networking fstab: /etc/fstab
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