Troubleshooting an empty output folder on the NextSeq 500/550 NCS 4.0

Windows 10 on NextSeq 500/550 systems upgraded to NextSeq Control Software (NCS) v4.0+ have additional requirements for connectivity to network shares. If system is not set up properly, sequencing runs may complete without errors and all data available in Temp folder, but no data available in the output folder.

Background:

• Can happen with local (D:\ or external USB drive) or networked server.

• Run completes without errors displayed in NCS.

• It is independent of chosen run mode set up (Local Run Manager (LRM) or Manual.

• Full run data generated in local Temp run folder (D:\Illumina\NextSeq Control Software Temp)

Troubleshooting steps:

• Manually transfer run data files from original Temp folder (D:\Illumina\NextSeq Control Software Temp[Run ID]) to the output directory.

• Ensure the system is set with correct folder depth rules

  • //[server]/folder1/

  • //[server]/folder1/folder2

  • D:[folder1][folder2]

• In case the system is not connect to the internet, disable the following setting under NextSeq Control Software > System Settings

  • "Send Instrument Performance Data to Illumina"

• If subsequent runs are still not transferred, follow the guidance on Knowledge Article Troubleshooting Universal Copy Server error on the NextSeq 500/550 (NCS 4.0+).

• If issue persists, contact Illumina Technical Support for further assistance.

For any feedback or questions regarding this article (Illumina Knowledge Article #5028), contact Illumina Technical Support [e-mail].