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davidemms / OrthoFinder

Phylogenetic orthology inference for comparative genomics
https://davidemms.github.io/
GNU General Public License v3.0
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Problem with ulimit -Hn. ERROR: The system limits on the number of files a process can open is too low. #848

Open Felipe-ia opened 1 year ago

Felipe-ia commented 1 year ago

I'm having trouble changing the ulimit -Hn. I already changed it to 188456 files but when I run it again, it asks to change it to 188456 again and it was already changed. CODE (orthofinder) fcasais@tyrion:/media/dragonstone/fcasais$ /home/fcasais/miniconda3/envs/orthofinder/bin/orthofinder -f /media/dragonstone/fcasais/4-Anotação_Prokka-2/Prokka_faa/

Best outgroup(s) for species tree

2023-08-23 03:17:30 : Starting STRIDE 2023-08-23 03:34:05 : Done STRIDE Observed 65 well-supported, non-terminal duplications. 65 support the best roots and 0 contradict them. Best outgroups for species tree:

WARNING: Multiple potential species tree roots were identified, only one will be analyed.

Reconciling gene trees and species tree

Outgroup: GCA_013415305 2023-08-23 03:34:05 : Starting Recon and orthologues 2023-08-23 03:34:05 : Starting OF Orthologues

ERROR: The system limits on the number of files a process can open is too low. For 434 species OrthoFinder needs to be able to open at least r=188456 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 188456
  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 188456 for user called 'emms' add the lines: emms hard nofile 188456 emms soft nofile 188456 (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 'from trees' using the '-ft' command

For full details see: https://github.com/davidemms/OrthoFinder/issues/384

ERROR: An error occurred, please review the error messages they may contain useful information about the problem.

Felipe-ia commented 1 year ago

(orthofinder) fcasais@tyrion:/media/dragonstone/fcasais$ ulimit -Hn 188456 (orthofinder) fcasais@tyrion:/media/dragonstone/fcasais$ ulimit -Sn 188456 See? It's already changed