NovaSeq 6000 File paths

Run folders The NovaSeq 6000 saves each run folder in three locations, with different files in each. The run folder locations and an overview of the contents are listed below. The file lists are not exhaustive.

1. Z:\outputfolder[run folder] Note: the Z drive does not include the RunParameter.xml file.

• Data folder (Intensities - BaseCalls - Lanes - Cycles)

• InterOp

• Logs (this is the only location that contains these RTA log files)

  • info_00000.log

  • warning_00000.log

• Thumbnail_Images folder (includes the first cycle of each read for tiles that end in 3)

• RTA3.cfg

• RTAComplete.txt

• RunInfo.xml

2. C:\ProgramData\Illumina\NovaSeq\NovaSeqTemp[run folder]

Note: The ProgramData folder may be hidden; to un-hide files, select the View tab in the file explorer window and make sure “Hidden items” is checked.

• Alignment Folder (contains Autocenter images)

• Config Folder

• Focus Model Folder

• InstrumentAnalyticsLogs Folder

• InterOp Folder

• Logs Folder

  • CIB Report folder

  • CompressedLogs folder - contains compressedlogs.zip file

  • ETF folder

  • FcBirdAnalysis folder

  • FlowCellFlatness folder

  • Pressure folder

  • UcsLogs folder - csv for run - .json file for run - Cycle Logs files - includes information on system thermal (Pump and compressor currents, fan speeds) activity and fluidics (pressure sensor readings, pump current, RCA valve positions) activity

  • Warnings and Errors Log files

  • Wash Log files (Wash.00.log) (shows run completed and wash completed successfully)

  • Run Setup Log files - chassis checks (reservoir levels, drip tray status, FC door, optics lid, BIM drawer, RCA drawer door and position, SOUR sensors, Autotilt operations) - Autotilt Report files - Focus Model Generation Report per surface (up to 2 files) - Thermal Report for run - logs all temperature readings every 10 seconds during each cycle - Thermal Report for post-run wash

• Recipe Folder

• RunComplete.txt

• RunInfo.xml

• RunParameters.xml

• SampleSheet.csv (if applicable)

3. Network Location (Output Folder) files

• Config folder

• Data folder

• InterOp folder

• Logs folder (this resembles C:\ drive run folder logs above; does not include RTA logs)

• Recipe folder

• Thumbnail_Images folder

• RTA3.cfg

• RunInfo.xml

• RunParameters.xml

• SampleSheet.csv (if applicable)

• RTAcomplete.txt

• CopyComplete.txt

Flags for the ends of run The NovaSeq 6000 generates files at the completion of select steps in the sequencing and primary analysis processes. The table below reviews the completion flag files and their file paths.

File Name	Time of creation	Location
SequenceComplete.txt	Created by NovaSeq Control Software once sequencing is complete	C:\ProgramData\Illumina\NovaSeq\NovaSeqTemp\[run folder] and Network output folder
CopyComplete.txt	Created once Universal Copy Service (UCS) completes data transfer	C:\ProgramData\Illumina\NovaSeq\NovaSeqTemp\[run folder]
RTAComplete.txt	Created once (Real Time Analysis) RTA3 has completed processing	Z:\outputfolder\[run folder] and C:\ProgramData\Illumina\NovaSeq\NovaSeqTemp\[run folder]

**Additional file paths

Run Setup Logs** - C:\ProgramData\Illumina\NovaSeq\NovaSeqTemp\RunSetupLogs

• Logs from the time when a flow cell side is selected through the pre-run checks.

• Contains folders for each run.

Maintenance Logs - C:\ProgramData\Illumina\NovaSeq\Illumina Maintenance Logs

• ZStage folder

• Temperature Logs for Green and Red Lasers

• MaintenanceLogFile.txt (includes wash log, which shows start/stop times of sequencing runs, post-run washes, and maintenance washes)

System Check Results - C:\Illumina\System Checks

If there is an issue with a run on the instrument, Illumina Technical support will request files for review. The table below lists types of investigations along with the files (with file paths) that may be requested by technical support.

The following file paths are for NovaSeq Control Software (NVCS) v1.5 and later.

Type of Investigation	Logs or Files Needed	Location
Failure to find fiducial	Auto center images	C:\ProgramData*\Illumina\NovaSeq\NovaSeqTemp\[RunFolder]\ Alignment
Run quality	SAV data	C:\ProgramData*\Illumina\NovaSeq\NovaSeqTemp\[RunFolder] InterOp Folder, RunInfo.xml, RunParameters.xml
Run aborted with error	SAV data	C:\ProgramData*\Illumina\NovaSeq\NovaSeqTemp\[RunFolder] InterOp Folder, RunInfo.xml, RunParameters.xml
Cycle logs	C:\ProgramData*\Illumina\NovaSeq\NovaSeqTemp\[RunFolder]\Logs
Data transfer to network or BaseSpace Sequence Hub	UCS logs and accessory files	C:\ProgramData*\Illumina\UniversalCopyService\

\*The ProgramData folder may be hidden. To un-hide files, select the View tab in the File Explorer window and make sure Hidden items is selected.

Once collected, reach out to Illumina Tech Support ([e-mail]) to request a file transfer link to upload the specified files and discuss next steps.

For any feedback or questions regarding this article (Illumina Knowledge Article #2426), contact Illumina Technical Support [e-mail].