Guide - MinION - Gsl_9165_v114_revb_13jul2022- 3/32

1.2

Before you start...

Need help?

Turn off sleep modes:

Navigate to Start > 'Settings' > 'System' > 'Power & Sleep'
Set 'Sleep modes' to Never

Ensure your computer is plugged into a power source.

Defer Windows upgrades:

Navigate to Start > 'Settings' > ' Update & Security' > 'Windows Update' > 'Advanced options'
Tick the Defer upgrades box

Note: on some versions of Windows, this will be called 'Pause updates'.

FAQ

Check that you have sufficient disk space. A typical Control experiment will require approximately 40 GB of space. However, for a full sequencing experiment using your own DNA or RNA sample, a minimum of 1 TB storage space is recommended. Please see this FAQ for more information.

Turn off your anti-virus for the software download steps. You can enable it again once the software is installed on your computer.

FAQ

Confirm with your IT department that you have the firewall settings described in this FAQ.

FAQ

If you are working behind a proxy, follow the instructions in this FAQ, and speak to your IT department before implementing any changes.

help

A minimum of 1TB internal SSD is required, because sequencing generates a large amount of raw current data which is written to disk in real time. These intermediate files are normally much larger than the final sequencing data. After the sequencing script has finished, these intermediate files will automatically get deleted and only your sequencing data will remain. This means that the I/O (input/output) performance of the system is key to ensuring no data is lost during the sequencing run. A smaller disk size or other disk types, such as HDD, external SSD or fusion SSD, tend to lead to sequencing run or computer crash and data loss.

Please note that the drive on which MinKNOW is installed MUST be a minimum 1 TB internal SSD drive, regardless of where you have set the MinKNOW output location. This FAQ contains instructions for changing the output location after installation.

The most common cause of "Please ensure your computer is connect" is a network or firewall issue. Please work with your IT department to ensure the following is allowed.

For the MinION, a quick test to see if the issue is your work network is to take your laptop home and see if the MinION is recognised on your home wifi network. Alternatively, for any sequencing device, you can tether/hotspot your mobile phone to your computer/device.

Refer to the MinION IT Requirements for information on Inbound and Outbound traffic and a list of IP addresses to whitelist.

To set up MinKNOW using a proxy please look at the following FAQ.

Once your proxy is set up and you have whitelisted all the necessary IP addresses, if you are still seeing this message, please follow the below instructions (Windows):

Click the Windows start button and type "Internet Options" - run the internet options app from the search results above
Click the "Connections" tab above, then the "Lan Settings" button found at the bottom of the dialogue box
Tick the "Bypass proxy server for local addresses" check box
Start the command prompt as administrator from the windows start menu (search for the command prompt, right click and chose "run as administrator" - type "net stop MinKNOWsvc" without quotes, wait for MinKNOW service to stop. Type "net start MinKNOWsvc" without quotes and wait for the MinKNOW services to restart.
Unplug and replug the MinION into your USB port, restart MinKNOW.

A proxy may be set by editing the user_conf file

Navigate to user_conf

Windows: C:\ProgramFiles\OxfordNanopore\MinKNOW\conf\user_conf
Mac: /Applications/MinKNOW.app/Contents/Resources/conf/user_conf
Ubuntu: /opt/ont/MinKNOW/conf/user_conf

Edit this portion:

"proxy": {
"cereal_class_version": 0,
"use_system_settings": true,
"auto_detect": true,
"auto_config_script": "",
"https_proxy": "",
"proxy_bypass": ""

https_proxy should be in the style of:
scheme://[username:password@]host:port or "http://domain\\username:password@host:port", where "scheme" is one of https, socks, socks4 or socks5.