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jiarong / VirSorter2

customizable pipeline to identify viral sequences from (meta)genomic data
GNU General Public License v2.0
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error when increase the threads for hmmsearch #79

Closed mujiezhang closed 3 years ago

mujiezhang commented 3 years ago

Hi, I am using VirSorter2 to predict viruses from bacteria genomes. I want to speed up it and run the command "virsorter config --set HMMSEARCH_THREADS=4". Then I got the following error:

(vs2) [clsjhh@login2 ~]$ virsorter config --set HMMSEARCH_THREADS=4 [2021-07-07 22:11 INFO] VirSorter 2.2.2 [2021-07-07 22:11 INFO] /lustre/home/acct-clsjhh/clsjhh/anaconda3/envs/vs2/bin/virsorter config --set HMMSEARCH_THREADS=4 Traceback (most recent call last): File "/lustre/home/acct-clsjhh/clsjhh/anaconda3/envs/vs2/bin/virsorter", line 10, in sys.exit(cli()) File "/lustre/home/acct-clsjhh/clsjhh/anaconda3/envs/vs2/lib/python3.8/site-packages/click/core.py", line 1137, in call return self.main(args, kwargs) File "/lustre/home/acct-clsjhh/clsjhh/anaconda3/envs/vs2/lib/python3.8/site-packages/click/core.py", line 1062, in main rv = self.invoke(ctx) File "/lustre/home/acct-clsjhh/clsjhh/anaconda3/envs/vs2/lib/python3.8/site-packages/click/core.py", line 1668, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/lustre/home/acct-clsjhh/clsjhh/anaconda3/envs/vs2/lib/python3.8/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, ctx.params) File "/lustre/home/acct-clsjhh/clsjhh/anaconda3/envs/vs2/lib/python3.8/site-packages/click/core.py", line 763, in invoke return __callback(args, **kwargs) File "/lustre/home/acct-clsjhh/clsjhh/anaconda3/envs/vs2/lib/python3.8/site-packages/virsorter/virsorter.py", line 925, in config val = os.path.abspath(val) File "/lustre/home/acct-clsjhh/clsjhh/anaconda3/envs/vs2/lib/python3.8/posixpath.py", line 374, in abspath path = os.fspath(path) TypeError: expected str, bytes or os.PathLike object, not int

I do not know the reason...

jiarong commented 3 years ago

Hi, I can not reproduced the error.. You might have config file from previous versions. You can use the following command to locate it and change "HMMSEARCH_THREADS" directly in it.

mujiezhang commented 3 years ago

Thanks you! I reinstalled virsorter2, and resolved it. But I wonder why the HMMSEARCH_THREADS is 2. Since the virsorter2 spend most of the run time in annotation, why do not set more threads for hmmsearch?

jiarong commented 3 years ago

The season for setting threads at 2 is that hmmsearch is not efficient at in using the cpus when the threads number is larger than 2. My experience is 4 is the maximum it can use in our server.