This is a test version of Biostars. For the public version, visit https://www.biostars.org.
ERROR: The system limits on the number of files a process can open is too low.

Hi, I am trying to run orthofinder on server and i also do the suggestion for following error and still facing same error. Does anyone know how to solve it ?

./orthofinder -ft /home/bvs/neelam/orthofinder/OrthoFinder/Results_Mar15_2 -t 4

OrthoFinder version 2.5.4 Copyright (C) 2014 David Emms

2022-03-21 09:33:13 : Starting OrthoFinder 2.5.4 4 thread(s) for highly parallel tasks (BLAST searches etc.) 1 thread(s) for OrthoFinder algorithm

Checking required programs are installed

Test can run "fastme -i /home/bvs/neelam/orthofinder/OrthoFinder/Results_Mar15_2/WorkingDirectory/SimpleTest.phy -o /home/bvs/neelam/orthofinder/OrthoFinder/Results_Mar15_2/WorkingDirectory/SimpleTest.tre" - ok

Running Orthologue Prediction

Reconciling gene and species trees

2022-03-21 09:33:23 : Starting OF Orthologues

ERROR: The system limits on the number of files a process can open is too low. For 359 species OrthoFinder needs to be able to open at least r=128981 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 128981
  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 128981 for user called 'emms' add the lines: emms hard nofile 128981 emms soft nofile 128981 (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.

Thank you!

orthofinder
• 2,288 views • link
written by Neel • Neel

The program is telling you everything you need to do, which is run the ulimit command and find out what your file limit is, and then increase it if needed. You may need to ask the admin to do this for you if you don't have the privilege.

• 0 views • link
written by Mensur Dlakic Mensur Dlakic

Thank you for your time, I had already done this by using this commands ulimit -n 128981 but it doesn't solve anything. Now i understand that i have to tell admin for root privilege.

Thank you so much!

• 0 views • link
written by Neel • Neel

0 answers

No answers yet.

Log in to answer this question.

More posts like this