Comment on page

Troubleshooting MiSeq washes taking extended time to complete

If a MiSeq wash is taking too long to complete, it is possible the MiSeq has had a communication error and the wash has stalled.
To Troubleshoot:
  1. 1.
    Confirm which wash was intended and how long ago it was started. Verify time in the wash is longer than what is expected for the type of wash.
  • Post-run wash: 20 minutes or 30 minutes, if using the template line wash option.
  • Maintenance wash: 90 minutes (3 steps - 30 minutes each step).
  • Standby wash: 120 minutes (2 steps - 60 minutes each step).
  1. 2.
    Power cycle* the MiSeq.
  • If the control software is responsive, exit the wash and shut down the MiSeq.
  • If the control software is not responsive, open the task manager to end the task for MiSeq control software via the following pathway: Task Manager > Processes > MiSeqSoftware.exe > End Task.
    • Open the task manager by right-clicking in the taskbar and select task manager or by pressing CTRL +ALT+DEL and select task manager.
  • Shut down MiSeq through the Windows start menu, and toggle the power switch at the back of the instrument to the OFF position. Leave powered down for a full minute.
  1. 3.
    ​​​​​​​After turning the instrument back on, if the instrument initializes without errors, repeat the wash that was in progress and monitor the time to complete.
  2. 4.
    If there are errors during system re-initialization or if the wash gets stalled again, contact Illumina Technical Support for further assistance.
*For further information, search for Knowledge Base articles Wash best practices for MiSeq, How to Shut down or power cycle the MiSeq, and How To Power Cycle the MiSeq Video.
For any feedback or questions regarding this article (Illumina Knowledge Article #2083), contact Illumina Technical Support [email protected].
© 2023 Illumina, Inc. All rights reserved. All trademarks are the property of Illumina, Inc. or their respective owners. Trademark information: Privacy policy: