RTA (Real-Time Analysis) is an integrated software that analyzes flow cell images and calculates metrics during a run. You may need to manually stop and restart RTA if it is stalled or if the network path is down.

Note that the HiSeq 3000/4000, HiSeq X, MiniSeq, NextSeq 500/550, iSeq 100 and NovaSeq 6000 sequencing platforms use different versions of RTA that cannot be restarted.

To restart RTA on the MiSeq:

1. To confirm that RTA has not completed, verify 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. You can minimize this window.

To restart RTA on the HiSeq 2500:

Note that the D drive is for flow cell A, and the E drive is for flow cell B.

1. To confirm that RTA has not completed, verify that there is no RTAComplete.txt file present in the run folder (D:\Illumina\HiSeq Temp\<run folder>, or E:\Illumina\HiSeq Temp\<run folder>).
2. To terminate the current RTA, locate the large RTA window that has both Tile Status and Log Output tabs for the run. Select the Log Output tab.
3. On the Log Output tab, select all four or eight Pause boxes (a checkmark indicates a paused task), and then select Terminate RTA.
4. Select Yes to confirm.
5. To restart RTA, double-click the RTAstart.bat file, located in D:\Illumina\HiSeq Temp\<run folder>\Config, or E:\Illumina\HiSeq Temp\<run folder>\Config.
6. Two windows open, confirming that RTA has been restarted. These windows can be minimized.

You can email Illumina Technical Support at techsupport@illumina.com with questions, or if you run into any trouble restarting RTA.