File paths for the NextSeq 500/550

The run folders on the NextSeq 500/550 include run data, along with many files that are helpful for reviewing run performance and troubleshooting, if necessary.

NextSeq Control Software (NCS) 2.2.x and 4.0.x Run Folder: The file path of each run folder is:

• D:\Illumina\NextSeq Control Software Temp[Run_Folder]

Key files in this location include:

• Runinfo.xml

• Runparameters.xml

• InterOp folder

• Thumbnail Images

• SampleSheet.csv

• Cycle Logs:

  • (D:\Illumina\ NextSeq Control Software Temp [Run_Folder]\Logs)

• Diagnostic.00.log:

  • (D:\Illumina\ NextSeq Control Software Temp [Run_Folder]\Logs)

• Focus Images:

  • (D:\Illumina\ NextSeq Control Software Temp[Run_Folder]\Images\Focus\L00X\C1.1)

• RTA Logs:

  • (D:\Illumina\ NextSeq Control Software Temp[Run_Folder]\RTALogs)

• RTA Config:

  • (D:\Illumina\ NextSeq Control Software Temp[Run_Folder]\Data\Intensities\RTAConfiguration.xml)

• FirmwareVersions.txt:

  • (D:\Illumina\ NextSeq Control Software Temp[Run_Folder]\Config)

• DemultiplexSummaryF1L1.txt

  • (Generated after FASTQ generation completes): [run folder]\Alignment_#[date and time folder]

BCL Files (raw data output from sequencing) are saved in 2 locations:

• D:\Illumina\NextSeq Control Software Temp[Run Folder]\Data\Intensities\Basecalls

• [Output Folder][Run Folder]\Data\Intensities\Basecalls

Additional helpful file paths:

• NCS Logs in Windows 7: (C:\Illumina\NextSeq Control Software\Logs)

• NCS Logs in Windows 10: (D:\Illumina\NextSeq Control Software\Logs)

• Maintenance Logs: (D:\Illumina Maintenance Logs)

• Preventative Maintenance (PM): D:\Illumina\PreventativeMaintenance

• NextSeq Control Software Config: (C:\ProgramData\Illumina\NextSeq Control Software\InstrumentShell.NextSeqControlSoftware.Options.cfg)

• BaseSpace Broker Logs: D:\Illumina\BaseSpace broker (NCS 2.2.x only)

• Restart Universal Copy Service (UCS): (C:\ProgramFiles\Illumina\UniversalCopyService\ucs.exe) (NCS 4.0.x only)

• System Check Results (all): D:\Illumina\SystemCheckResults

Beadarray folder: (The NextSeq 550 can be used to scan select beadarrays.)

• [Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode]\Config folder

• [Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode]\Focus folder

• [Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode]\Logs folder

• [Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode]\GTC files

• [Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode]\IDAT files

• [Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode]\Image files

• [Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode][Barcode]_sample_metrics.csv

• [Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode][Barcode]_section_metrics.csv

• [Date]_[Instrument Name]_[Scan#]_[Barcode]\ScanrParameters.xml

For any feedback or questions regarding this article (Illumina Knowledge Article #2072), contact Illumina Technical Support [e-mail].