Subprocess command depends on OS

WrightonLabCSU / CAMPER

This is a repository for CAMPER.

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Subprocess command depends on OS #5

Open ParsaGhadermazi opened 5 months ago

ParsaGhadermazi commented 5 months ago

Hi,

Thanks for making this great tool available. When running on MacOS, I get an error in the following line:

run_process(['mmseqs', 'createindex', output_loc, tmp_dir, '--threads', str(threads)], verbose=verbose)

I guess this is happening because the command argument for run_process is different depending on the OS (A list of strings vs. a single string)

Parsa

houjialin commented 5 months ago

Hi, I got similar error in our CentOS system with following information:

raise CalledProcessError(retcode, process.args,
517 subprocess.CalledProcessError: Command '['mmseqs', 'createindex', 'CAPMER_annotation/working_dir/bin.9/gene.mmsdb', 'CAPMER_annotation/working_dir/bin.9/tmp',  
    '--threads', '10']' returned non-zero exit status 1.

Jialin

KatherineDuchesneau commented 2 months ago

Hi Parsa and Jialin,

I think the issue is that the input fasta file for the standalone camper module has to be in amino acid sequences. Make sure that you are using a translated file and the mmseqs command should work.

Best, Kat

ParsaGhadermazi commented 3 weeks ago

Hi Kat,

Thanks. This solved the problem.

Best, Parsa