How to stop and restart RTA on the MiSeq

RTA (Real-Time Analysis) is an integrated software that analyzes flow cell images and calculates metrics during a sequencing run, converting those images into BCL files.
The pre-processed images captured by the instrument are large in size. As such, if RTA is not restarted and there is not an adequate amount of disk space available to store the images, the run may crash as a result.
If RTA stalls or the network path is down, the following error message may appear:
When this notification occurs, follow the instructions below:
  1. 1.
    Close the notification or select Close the program.
  2. 2.
    Select Pause on the run in the Control Software.
  3. 3.
    Manually stop and restart RTA.
  • To restart RTA on the MiSeq: 1. Confirm that RTA has not completed by verifying that there is no RTAComplete.txt file present in the run folder (D:\Illumina\MiSeq Temp[run folder]). 2. Select the Windows Start button (bottom left of the computer screen), and search for Task Manager. * Alternatively, press Ctrl+Alt+Delete on the keyboard to open Task Manager. 3. In Task Manager, select the Processes tab, right-click on RTA.exe, and select End Process. 4. To restart RTA, double-click the RTAstart.bat file, located in D:\Illumina\MiSeq Temp[run folder]\Config. 5. Confirm that RTA.exe is present in the Task Manager Processes tab. * Note: A small black command prompt window indicates that RTA is running, and it can be minimized.
  1. 4.
    Once RTA has been restarted, select Resume on the run in the Control software.
For further information on data processing by RTA, search for Knowledge Base article MiSeq output and analysis folder quick reference guide.
For additional guidance, contact Illumina Technical Support.
For any feedback or questions regarding this article (Illumina Knowledge Article #2031), contact Illumina Technical Support [email protected].
Last modified 23d ago
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