Number of files in the work folder

[esud1]

Hello,

Thank you for your previous help!
I can now run the analysis, but kind of hindered by the huge number of files in the work folder.
Since I am running on the university cluster, I am limited to the number of files allowed on the server.
Are there any ways to reduce this huge file numbers in the work folder?

Thanks!
Edi

[sinamajidian]

Hi Edi
you're welcome. I'm not sure we have a solution for this right now.
How many species are you working on?
Is the limitation on the total number of stored files or
the number of files that are open at a time?
For the latter, one idea is to increase the limit with ulimit -n 271072 if the system allows.
(There will be many more files if --write_msas --write_genetrees are activated, which is not by default).
Best,
Sina

[alpae]

note that you can specify a different folder for the work directory. often there is a scratch space that allows more files per user. you can set this with the -work-dir command line option.