Port Reset and Power Cycle Sequence for iScan or HiScan, without an AutoLoader

Before starting:

• Make sure that the computer's local (C:) hard drive has free memory space and is not full.

• Check that the iScan is plugged in with no loose cables.

• Try restarting the iScan computer by selecting Start > Restart, instead of Shut Down, then attempt to start the iScan Control Software (ICS).

Use Device Manager to clear the ports, then power cycle the instrument and computer in the following order:

1. Close ICS and leave the iScan on. If necessary, use Task Manager to force-quit ICS and other open programs.

2. Launch Device Manager. Using the Windows Search or Control Panel Search, type 'Device Manager' and select the program to open it.

3. In Device Manager, navigate to Ports (COM & LPT).

4. The number of ports listed in Device Manager will depend on the model of the iScan computer (Figure 1):

Figure 1: List of expected number of ports for each iScan computer model and example of 18 ports listed in Device Manager for a DC Fortris A8202 computer. 5. Starting at the bottom of the port list, right-click on the port, and select 'Uninstall Device'. For example, in Figure 1, start with (COM9). If prompted, check the 'Delete the drivers software for this device' option then select 'OK'. 6. Repeat this process to uninstall all COM ports except for Communication Port (COM1) and Phoenix Serial Port (typically COM 3 or COM7, Figure 2):

Figure 2: All ports removed, except for COM1 and Phoenix Serial Port. 7. Turn the scanner OFF using the hard switch on the back of the instrument. 8. Sometimes ports will re-populate when the scanner is shut off (Figure 3). Uninstall remaining ports in Device Manager.

Figure 3: Example of ports re-populating after iScan is turned off. 9. Turn the computer OFF by selecting Shut Down from the Start menu and wait 3 minutes. 10. Restart the computer and let the computer fully reboot (~2 minutes). 11. When the computer is fully booted, turn the scanner ON. 12. In File Explorer, open My Computer or This PC and confirm that the iScan 'Archimedes'/'Do Not Eject' drive is detected. This drive must be recognized by the computer before opening ICS. 13. Open Device Manager and confirm that the expected amount of ports are populated, and that there are no duplicate or missing ports. 14. Start ICS and scan the beadchips.

For any feedback or questions regarding this article (Illumina Knowledge Article #1492), contact Illumina Technical Support [e-mail].