Tutorial:Using the MinION MinKNOW software on Ubuntu 1604

Question

[colindaven]

We recently set up a Minion here on Ubuntu 1604 and had to piece together the technical details for the command line, so here they are.

Computer needed

• 1 TB SSD drive minimum.
• Optimally with Ubuntu OS installed on the same 1 TB drive.
• Install MinKNOW via the instructions on the ONT community website
• We do not do on the fly base-calling, but just use the machine for data collection
• After data collection we do base-calling using SLURM https://github.com/colindaven/guppy_on_slurm
• Never plug another USB stick etc into the computer. This always messes up the USB MinION connection.

Setting up the proxy server

# remember to do this after every MinKNOW update!
cd /opt/ont/minknow/conf
sudo nano user_conf

# The last section should look like this: September 2019
# Obviously change the "https_proxy" line to your proxy

      "proxy": {
        "cereal_class_version": 0,
        "use_system_settings": false,
        "auto_detect": false,
        "auto_config_script": "",
        "https_proxy": "proxy.my-university.de:8080",
        "proxy_bypass": ""
    }

Starting MinKnow

# Start service
cd /opt/ont/minknow
nohup sudo bin/mk_manager_svc &

# Some users start the MinKNOW service like this
sudo service minknow start

# Start MinKNOW GUI
nohup /opt/ont/minknow-ui/MinKNOW &

Stop MinKNOW

# Stop GUI. Don't forget to stop the minknow service which keeps in running status even after stopping minknow
sudo service minknow stop

# This command will give you a Process ID, eg 12345, which you can use kill on directly to stop the process
ps -aux | grep MinKNOW 
kill 12345

## Make sure service stopped before restarting to include new config changes, eg proxy
ps -aux | grep manager
sudo kill 12345

Happy sequencing!

2019 version for backwards compatibility:

Note - some of the old paths were correct in 2019 but changed to lower case in a new MinKNOW

# old 2019 version
#cd /opt/ONT/MinKNOW/conf

cd /opt/ONT/MinKNOW
nohup sudo bin/mk_manager_svc &

nohup /opt/ui/MinKNOW &

[Rox]

Cool tutorial ! I was always hesitating on making some Nanopore content on Biostar, because I thought the Nanopore community was "closed" and I thought it wasn't allowed to share informations outside of the community forum. Otherwise, a Guppy tutorial would be more than needed I think, unless it already exist and I did not saw it :). I could try to make one !

[colindaven]

Thanks! Hmm, wouldn't such a policy go against a) twitter, which the company and associates use widely to promote their technology b) being one of the companies with the biggest number of distributed sequencers (minions) and c) AFAIK the community is open to anyone who wants to register these days, since a colleague joined recently with email only.

I think anyone helping making bioinformatics easier for ONT technologies is going to greatly benefit the company. If they object, it can be taken down though.

[Rox]

Alright then, as soon as I'll gather enough information, I'll make a tiny tutorial for Guppy :)

[lakhujanivijay]

Thanks colindaven

Don't forget to stop the minknow service which keeps in running status even after stopping minkow

sudo service minknow stop

To start the service again

sudo service minknow start