– If the computer needs to be switched off and/or restarted it is always best to remove the MinION and then proceed with the shut down. This applies even in normal circumstances where the customer is finished with the computer and would like to shut it down.
-It is always best to restart the computer in between runs, whether this is shut down after a run or restarted/power-cycled before a new run is begun. Again in all cases, make sure the MinION is not plugged in.
-If the MinION was left in and you open MinKNOW you may find some errors such as “no host found” or “cannot connect to host”. You might also see the message “please insert a MinION to get started”. If you see any of these errors it is best to unplug and replug the MinION in. Give the software a moment and the device should register again on the Software Overview page.
-In some cases when a MinION is plugged in or if a MinION was left in while the computer was turned off/on again you might also see a MinION graphic/image in the Software Overview page with a “Connection error” message. If you see this you can unplug the MinION and reattach or, better, right click the image and select the “Restart position” option. This will refresh the graphic and you should now see the normal MinION/flow cell image.
-You can also Restart Position if you see the MinION image but it says there is no flow cell (and you have a flow cell inserted). You can either restart the position or physically take the flow cell out of the MinION and put it back in again
-If there is a run error within the first few minutes of the sequencing run starting (“Run stopped with error”, “Run stopped due to internal error”), you can also Restart the position and set-up the run again, or restart the computer entirely (remembering to unplug the MinION first). The flow cell and library will not be affected. Ensure also the flow cell is inserted correctly into the device and ensure the device/usb cable is connected properly to the laptop. It is best also to ensure the usb cable is not being strained and that the MinION is kept close to the computer – stretching of the cable can lead to disconnection.

If sequencing errors persist or if you want to delve further into an error that was not resolved by any of above, you can find the logs for the device and send them to us or have your IT team take a look first. The logs can be found here:
/var/log/minknow/MNXXXXX