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Description
I'm trying to make a marker file for Haemophilus parasuis. I have been using this format:
checkm taxon_set <rank> <taxon> <marker file>
In the terminal I use:
checkm taxon_set species Haemophilus parasuis haemophilusparasuis.ms
It always gives me this error:
(checkm_v1_2_4) jimwel_bioassets@bioassets-corp:/mnt/c/Users/JimwelBryanChristoph/Desktop/analysis_files/20260110_GPScgMLST_creation$ checkm taxon_set species Haemophilus parasuis haemophilusparasuis.ms /home/jimwel_bioassets/miniconda3/envs/checkm_v1_2_4/lib/python3.11/site-packages/checkm/checkmData.py:25: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. from pkg_resources import resource_filename usage: checkm {data,tree,tree_qa,lineage_set,taxon_list,taxon_set,analyze,qa,lineage_wf,taxonomy_wf,gc_plot,coding_plot,tetra_plot,dist_plot,gc_bias_plot,nx_plot,len_hist,marker_plot,unbinned,coverage,tetra,profile,ssu_finder,merge,outliers,modify,unique,test} ... checkm: error: unrecognized arguments: haemophilusparasuis.ms
How do you properly call the command for this? I tried getting rid of the space in "Haemophilus parasuis" and tried "_" symbol but it still does not work.