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I'm new in linux, Today I've logged in to my server and found that my 2TB drive is 95% full, which sounds incredible, and all services are down, the only access I have right now is SSH, I did try to find where are this files using df -H it show me in: /dev/vda1 , but going trough all folders will take ages.

how can I find easily where are the files and what causes the issue?

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All you need is 

du -msh /*

it will shows which directory, then follow the biggest size, for instance: 

du -msh /var/*

then 

du -msh /var/www/*

so on..

The reason can be anything, from upload of some files by users if you have them to log files caused by some error etc.

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