Error in The system limits on the number of files in the Orthofinder

Question

[K.Gee]

Hi, I'm running Orthofinder with the following command:

python  orthofinder.py  -f folder/

I tested with 5-6 files on the folder and worked perfectly.

My issue starts when I add 117 files (same format) in the same folder. After I typing the above command I am getting the following:

ERROR: The system limits on the number of files a process can open is too low. For 117 species OrthoFinder needs to be able to open at least r=13789 files. Please increase the limit and restart OrthoFinder
1. Check the hard and soft limits on the number of open files for your system:
    $ ulimit -Hn
    $ ulimit -Sn
2. If hard limit, h > r already, then you just need to increase the soft limit:
    $ ulimit -n 13789
3. Alternatively, if h < r then you need to edit the file '/etc/security/limits.conf', this requires root privileges. To increase the limit to 13789 for user  called 'emms' add the lines:
    emms hard nofile 13789
    emms soft nofile 13789
    (edit these lines to match your username)
4. Check the limit has now been updated (if you changed the hard limit you'll need to open a new session and confirm it's updated):
    $ ulimit -Sn
5. Once the limit is updated restart OrthoFinder with the original command

I also tried to increased the threads number but I got the same error.

Does anybody know how step this issue? Do I have to edit something to the system "root privileges" or I can step over with a command typing? I'm not so familiar with the Linux so I am afraid to edit something with the wrong way into the system.

Thank you in advance!!

[lieven.sterck]

did you do what it says? == checking the ulimit values?

depending on how your system has been setup it might very well be that you have to ask the admin to change those limits.

[K.Gee]

I see... thank you very much for the reply :-)