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jiarong / VirSorter2

customizable pipeline to identify viral sequences from (meta)genomic data
GNU General Public License v2.0
225 stars 31 forks source link

using one core? #83

Closed rotoscan closed 3 years ago

rotoscan commented 3 years ago

Dear developers,

thanks for this very interesting tool!

I am running on shared HPC using a job manager (SLURM) and I would like to know if its possible to control the number of spawned threads?

By checking config.yaml file I was able to see the variables that control the number of threads used for the tool, hmm, and so on.

$ cat ./virsorter2-conda/lib/python3.9/site-packages/virsorter/template-config.yaml | grep THREAD GENERAL_THREADS: 1 HMMSEARCH_THREADS: 2 CLASSIFY_THREADS: 1

What is the minimum number of threads virsorter2 needs to be used? 2? So, if I reserve only 2 threads for my job, should I set HMMSEARCH_THREADS abd 1 leave the rest at it is. Correct?

Thanks for any input!

Best Rodolfo

jiarong commented 3 years ago

Hi, the minimal number of threads VirSorter2 need is the max of the three numbers. I would add one more to be safe.