Key functionalities in Pycharm are not working as they should

Since few days I have noticed that my IDE is not acting as it should. I have no idea what can be the cause of it. I don't remeber doing something different than usual. Some key problems I'm facing:

• when using find usage in files no results are shown (even though I now that it is present in project and previously it was working)
• IDE is not suggesting anything when typing
• when using ctrl+b on some code snippet nothing is happening (previously I could jump to the usage of it) -analyzing some file is always in progress and does not show any results

Thinks I tried, but didn't work:

• invalidate caches and restart
• unistalled pycharm and installed it again (previously I have installed pycharm using snap, now I'm using toolbox)
• delete project and clone it again with new virtualenev
• also tried rescaning indexes, but it takes forever and even after leaving it over a night it is not finished

If it is important I have my pycharm installed on ubuntu inside Virtual Machine. Do you have any idea how else could I repair it?