distarch | Java分布式系统架构。包括分布式锁，一致性哈希，分库分表，单点登录，缓存，消息队列等 | Hashing library

You must grant write privileges to actual dbPath (in your case /home/vojtam/disk/mongodb) but also to all parent folders.

Home directories like /home/vojtam are usually accessible only for the owner, that's why they are called "home directory". The permissions of any sub-folder does not matter.

By default MongoDB process runs by user mongod, and typically a service is provided to any user of a system. Thus you should prefer a common folder for example /var/lib/mongo as used in defaults.

According this line

When you run mongod then MongoDB process is started with default parameters, see https://docs.mongodb.com/manual/reference/program/mongod/

However, when you run systemctl start mongod then systemd loads service file /usr/lib/systemd/system/mongod.service (check with systemctl status mongod). When you check this service file then you see that process is started as mongod -f /etc/mongod.conf, i.e. it uses the config file /etc/mongod.conf.

The settings in this config file can be different than mongod default parameters, see What is the default database path for MongoDB?

Note, if you like to customize your Mongo service, then you should not edit service file /usr/lib/systemd/system/mongod.service directly. Instead, make a copy to /etc/systemd/system/mongod.service and modify this copy according to your preferences. Otherwise when you upgrade MongoDB, the installer may revert /usr/lib/systemd/system/mongod.service file to default values.

Folders in this answer apply to Redhat Linux, they may be different on Ubuntu. Have a look at your system documentation.

Normally this is caused because you didn't start the mongod process before you try starting the mongo shell.

Start mongod server

This line say it all:

I tried in mongo 4.2.17, your insertion of documents yields a document like:

Please, change the following line in the .env file:

The answer is for other people who encountered this.

So basically service mongod start didn't run using root user.

And I don't know when it have been changed.

However you need to lookup the user in /lib/systemd/system/mongod.service

In my case is mongodb

Then run

sudo chown -R mongodb:mongodb {your_log_path} {your_db_path}