Troubleshooting MiSeq Control Software (MCS) v4 stalling during initialization

This issue has been observed when power cycling MiSeq after a run stopped with errors resulting in issues with data uploads to BaseSpace Sequencing Hub or the network. The issue is usually related to Universal Copy Service (UCS), where the .json contract files do not switch out of the 'Active' state when a run ends unexpectedly or there are network transfer issues.

Troubleshooting steps:

1. Contact Illumina Technical Support and provide the following files and information:

   1. MiSeq Control Software Logs: D:\Illumina\MiSeqControlSoftware\ Logs

   2. Universal Copy Service Logs: C:\ProgramData\Illumina\UniversalCopyService\Logs

   3. Collect all available UCS .json contract files: C:\ProgramData\Illumina\UniversalCopyService\Runs

   4. Requested information:

   5. Was there a run failure preceding the issue? If so, what kind of run failure?

   6. Was the MiSeq Control Software re-initialized before power cycling the instrument?

   7. Was the run folder deleted before power cycling the instrument?

2. Next, complete the following steps:

   1. Minimize the MiSeq Control Software (select the dropdown menu in the top left corner, then select Minimize).

   2. In the Windows Search bar, type Task Manager, then right-click on the App and select Run as Administrator.

      1. Enter the sbsadmin password if prompted.

   3. Use Windows Task Manager to close the MiSeq Control Software (MCS) by right-clicking MiSeq Control Software and selecting End task.

   4. In Task Manager, select the Services tab and scroll down to locate Universal Copy Service, then right-click on Universal Copy Service and select Stop.

   5. In a File Explorer browser window, navigate to C:\ProgramData\Illumina\UniversalCopyService\Runs.

   6. Remove old .json files by either deleting them from the Runs folder or creating a subfolder titled "ArchivedRuns" and moving the files into the newly created folder.

   7. Re-start UCS by right-clicking on Universal Copy Service in the Services tab in the Task Manager and selecting "Start" or "Restart."

   8. Re-launch the MiSeq Control Software.

For any feedback or questions regarding this article (Illumina Knowledge Article #5502), contact Illumina Technical Support [e-mail].