Troubleshooting Free Disk Space errors during Pre run Checks on MiSeq

If available disk space is low, a message appears and will prevent run setup from proceeding. A total of 100 Gigabytes (GB) available is required on the D:\ drive to start a sequencing run. The warning message will indicate how much space is required to meet the minimum threshold.

Troubleshooting steps:

1. Minimize the MiSeq Control Software (MCS).

   1. For MCS v3.1 and below, select the Minimize in the top right corner of the control software window.

   2. For MCS 4.0 and above, select the dropdown menu in the top left corner, then select Minimize Application.

2. In the Windows Operating System (OS), open the File Explorer application and navigate to the D:\Illumina folder.

3. Run folders can be deleted from the following sub-folders:

   1. D:\Illumina\MiSeqAnalysis

   2. D:\Illumina\MiSeqOutput

   3. D:\Illumina\MiSeqTemp

4. The Windows Recycle Bin must be emptied before the Pre-Run checks can be performed again.

Note: Deleted files and folders cannot be recovered once they are deleted from the instrument. Make sure that all needed files are backed up off-instrument.

For persisting disk space warnings on MiSeq instruments running MCS v4.0 on Windows 10 only, see the following additional actions.

Troubleshooting Persisting Disk Space warnings on MCS v4.0

Illumina software will leverage three applications that run as Services to handle data analysis and copy to the output folder. If the instrument is configured to output data to the local D:\ drive, then these Services must be configured to login as Local System.

If these Services are not configured properly, MCS will often present one or both of the following warnings after updating the local user passwords.

If the warnings persist after following the steps above and sufficient space on the local D:\ drive is confirmed, use the following steps to continue troubleshooting this issue.

Troubleshooting steps:

1. Exit the MiSeq Control Software by selecting the dropdown menu in the top left corner and select Exit Application.

2. Open Local Run Manager.

3. Select Tools, then System Settings, then the Service Accounts tab.

4. Select the Local System radio button, and then select Save.

5. In the Update Service Account Confirmation popup, select Continue.

6. Restart the MiSeq Control Software and attempt run setup again.

For any feedback or questions regarding this article (Illumina Knowledge Article #3753), contact Illumina Technical Support [e-mail].