Troubleshooting Stalled Flow Rate Check on the MiSeq

Users attempting to start a MiSeq run may encounter the flow rate check taking longer than expected during the Pre-Run Checks. Typically, this step takes between 3-4 minutes. However, a 10-minute flow rate check is still considered normal. If this step takes >10 minutes, this may indicate that the control software has become unresponsive.

Troubleshooting Steps:

1. Force-close the Control Software through the Windows Task Manager

   1. Press Ctrl+Alt+Del and select Task Manager

   2. Locate MiSeq Control Software in the Task Manager and select "End Task". This will force the control software to close.

2. Power Cycle the MiSeq. For complete instructions, review the article How to Power Cycle the MiSeq.

3. Once the system re-initializes, attempt to start the run again with the same consumables.

If the flow rate check stalls again or initialization fails, contact Illumina Technical Support.

For any feedback or questions regarding this article (Illumina Knowledge Article #9288), contact Illumina Technical Support [e-mail].