> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/microarray/iscan/microarray-iscan-reference_material-list/000001502.md).
# Power Cycle and Port Reset Sequence for two iScans and one AutoLoader
This article provides guidance for troubleshooting communication issues in dual-scanner AutoLoader configurations by outlining the recommended procedures and correct sequence for performing a complete power cycle and resetting communication ports.\
**Before starting:**
* Ensure that the computer local hard drives have free memory space and are not full.
* Check that the instruments are plugged in with no loose cables.
**Section I: SHUT DOWN SYSTEM**
1. Close all programs on both iScan Personal Computers (PCs). 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 host iScan using the hard power switch.
4. Reset the COM ports in the host PC using PortManager 2.0. For instructions, follow steps 3-6 of **Section III:** **RESET COM PORTS**.
5. Turn off the host PC using the Start Menu > Shut Down.
6. Turn off the remote iScan using the hard power switch.
7. Reset the COM ports in the remote PC using Port Manager 2.0. For instructions, follow steps 3-6 of **Section III:** **RESET COM PORTS**.
8. Turn off the remote PC using the Start Menu > Shut Down.
9. Wait at least 3 minutes.
**Section II: RESTART SYSTEM**
1. Turn on the host PC and log in, if prompted.
2. Wait 2 minutes for the host PC to completely reboot.
3. Turn on the remote PC and log in, if prompted.
4. Wait 2 minutes for the remote PC to completely reboot.
5. Turn on the host iScan using the hard power switch.
6. Wait 1 minute.
7. Turn on the remote iScan using the hard power switch.
8. Wait 1 minute.
9. On the host 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. \
**Figure 1.** Contents of the iScan drive folder.
* If the iScan drive is detected, proceed to step 10.
* If not, the ports need to be reset again on both computers and both iScans must be power cycled. Repeat **Section I: SHUT DOWN** procedures starting with step 1.
* If the iScan drive is still not detected after a completing a second port reset and power cycle sequence:
* Power off the host iScan and host PC.
* Try reseating the USB cable at right hand side of the host iScan and on the back for the host PC, or try a different USB port on the host PC.
10. Turn on the AutoLoader using the hard power switch at the base.
11. Start the AutoLoader 2.x Service software on the remote PC:
* On the remote 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 as some icons may be hidden.
**Figure 2.** AutoLoader 2.x Service software icon in the Windows taskbar.
* If the icon appears in the taskbar:
* Right-click the icon.
* Select Start.
* If the icon does not appear in the taskbar:
* Locate and double-click the AutoLoaderService.exe file in the C:\Program Files\Illumina\AutoLoader Service folder.
* In the Illumina AutoLoader Service dialog box that opens, click the "…" button and browse to the folder where the iScan Control Software (ICS) is installed: C:\Program Files (x86)\Illumina\iScan Control Software.
**Figure 3.** Folder selection for the iScan Control Software installation in the **Illumina AutoLoader Service dialog box.**
* Select Start.
12. On the host PC, start the ICS. In a dual-reader configuration, ICS needs to be run only on the host PC.
13. ICS on the host PC will automatically detect the AutoLoader, then ask “Automatic scan is enabled on this system, do you want to use AutoLoader2x?”
**Figure 4.** Confirmation of AutoLoader2x usage.
14. Select "Yes" to run ICS in automatic mode (with the AutoLoader). ICS will verify the login information for one or both readers and the ICS welcome screen will open.
15. Proceed with scanning beadchips.
**Section III: RESET COM PORTS**
1. 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.
**Figure 5. Port Manager 2.0 installer.**
*
```
* If PortManager 2.0 is not available on the iScan PC, obtain a copy from Illumina Technical Support (techsupport@illumina.com).
```
````
* If OS compatibility error message is seen, select OK to acknowledge the message:
```
- Right click the PortManager\_v2.0.exe icon and select Properties.
- Select the Compatibility tab.
- Check the Run the program in compatibility mode for check box.
- 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):
```
**Figure 6.** PortManager\_v2.0.exe Properties dialog box displaying the Compatibility tab.
````
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 issue/error persists**, select the column header “Port Name” to sort the COM ports and verify the correct number of ports detected.
**Table 1.** List of iScan PC models and the expected number of ports.
| 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.
References:
[How to Perform a Port Reset on HiSeq and iScan Instruments Video](https://www.youtube.com/watch?v=hDMuwqaXNbg)
[AutoLoader 2.x User Guide](https://support.illumina.com/downloads/autoloader_2x_user_guide_\(15015394_a\).html)
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| *For any feedback or questions regarding this article (Illumina Knowledge Article #1502), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001502%20-%20Microarray%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |
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