Power Cycle and Port Reset Sequence for one iScan with one AutoLoader

Before starting:* Ensure that the computer local hard drive has free memory space and is not full.

• Check that the instruments are plugged in with no loose cables.

Section I: SHUT DOWN SYSTEM1. Close all programs on the iScan PC. Use Task Manager to force-quit open programs, if necessary. 2. Turn off the AutoLoader using the hard power switch at the base. 3. Turn off the iScan using the hard power switch. 4. Reset the COM ports in the iScan PC using PortManager 2.0. For instructions, follow steps 3-6 of Section III: RESET COM PORTS. 5. Turn off the iScan PC using the Start Menu > Shut Down. 6. Wait at least 3 minutes.

Section II: RESTART SYSTEM1. Turn on the iScan PC and log in if prompted. 2. Wait 2 minutes for the iScan PC to completely reboot. 3. Turn on the iScan using the hard power switch. 4. Wait 1 minute. 5. On the iScan PC, open This PC/My Computer to confirm that the iScan drive is detected. The iScan drive may be named Archimedes, DoNotEject, or as a letter drive. The iScan drive folder contents include:

• If the iScan drive is detected, proceed to step 10.

• If not, the ports need to be reset again on the iScan PC and the iScan must be power cycled. Repeat Section I: SHUT DOWN procedures starting with step 1.

• If the iScan drive is still not detected after completing a second port reset and power cycle sequence:

  1. Power off the iScan and iScan PC.

  2. Try reseating the USB cable on the right-hand side of the iScan and on the back for the iScan PC, or try a different USB port on the iScan PC.

10. Turn on the AutoLoader using the hard power switch at the base.

• Start the AutoLoader 2.x Service software on the iScan PC:Check if the AutoLoader 2.x Service software icon appears in the Windows taskbar on the lower right side of the screen, near the time. Expand all icons if necessary since some icons may be hidden.
• If the icon appears in the taskbar:

  1. Right-click the icon.

  2. Select Start.

• If the icon does not appear in the taskbar:

  1. Locate and double-click the AutoLoaderService.exe file in the C:\Program Files\Illumina\AutoLoader Service folder.

  2. In the Illumina AutoLoader Service dialog box that opens, click the “…” button and browse to the folder where the iScan Control Software is installed: C:\Program Files (x86)\Illumina\iScan Control Software.

  iii. Select Start.

12. On the iScan PC, start the iScan Control Software (ICS).

13. ICS on the iScan PC will automatically detect the AutoLoader, then asks “Automatic scan is enabled on this system, do you want to use AutoLoader2x?”

14. Select "Yes" to run ICS in automatic mode (with the AutoLoader). ICS will verify the login information and the ICS welcome screen will open. 15. Proceed with scanning BeadChips.

Section III: RESET COM PORTS1. Close iScan Control Software (ICS), if open. 2. Turn off iScan. 3. Launch PortManager 2.0 by double-clicking the icon on the iScan PC’s Desktop.

• If PortManager 2.0 is not available on the iScan PC, obtain a copy from Illumina Technical Support ([e-mail]).

• If OS compatibility error message is seen, select OK to acknowledge the message:

  1. Right-click the PortManager_v2.0.exe icon and select Properties.

  2. Select the Compatibility tab.

  3. Check the ‘Run the program in compatibility mode for’ check box.

  4. Select the iScan PC’s OS in the pull-down menu. If the OS is not listed in the pull-down menu, choose ‘Windows XP (Service Pack 3)’:

  

4. Select the first port and select "Remove Device". The ports do not have to be in sequential order to complete this process.

5. Repeat for each port until the port field is completely empty.

6. Select "OK" when finished.

• Continue with shut down procedures in Section I: SHUT DOWN SYSTEM.

• Continue with restart procedures in Section II: RESTART SYSTEM.

7. If the issue/error persists, select the column header “Port Name” to sort the COM ports and verify the correct number of ports detected.

iScan PC model	Expected Number of Ports
Dell	14
DC Fortris F7441	14
DC Fortris A8202	18

• If any of the ports are missing (aside from COM2), repeat Section III: RESET COM PORTS procedure starting at step 1.

For further information, see How to Perform a Port Reset on HiSeq and iScan Instruments Video and the AutoLoader 2.x User Guide.

For any feedback or questions regarding this article (Illumina Knowledge Article #6785), contact Illumina Technical Support [e-mail].