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checkm don't recognize output directory when i add plot argument #409

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ShevchenkoAlla opened this issue Jan 31, 2025 · 0 comments
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@ShevchenkoAlla
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Hello,
I have an interesting situation
When I use code without plot checkM workes perfectly and provides a lof of output tables, but when I add plot option it cant recognize output dirrectory.

I really want to get plots, can anyone help me with that?

Are there any code that would provide all plots available?
Like it says here - Save all plots: The user has the option of generating and downloading all possible plots from the CheckM lineage workflow. Note that selecting this option will slow down the runtime (perhaps 10-20%).
https://narrative.kbase.us/legacy/catalog/apps/kb_Msuite/run_checkM_lineage_wf

So, I used:
"""
/home/miniconda3/bin/checkm lineage_wf bin_qa_plot -t 16 -x fa /home/spades_assembly/metabat2_dir/bin/ /home/spades_assembly/metabat2_dir/bin/checkm_bins
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: /home/spades_assembly/metabat2_dir/bin/checkm_bins
"""
But when I delete bin_qa_plot:
"""
/home/miniconda3/bin/checkm lineage_wf -t 16 -x fa /home/spades_assembly/metabat2_dir/bin/ /home/spades_assembly/metabat2_dir/bin/checkm_bins
[2025-01-31 20:00:34] INFO: CheckM v1.2.3
[2025-01-31 20:00:34] INFO: checkm lineage_wf -t 16 -x fa /home/spades_assembly/metabat2_dir/bin/ /home/spades_assembly/metabat2_dir/bin/checkm_bins
[2025-01-31 20:00:34] INFO: CheckM data: /home/miniconda3/checkm_data
[2025-01-31 20:00:34] INFO: [CheckM - tree] Placing bins in reference genome tree.
[2025-01-31 20:00:35] INFO: Identifying marker genes in 18 bins with 16 threads:
Finished processing 16 of 18 (88.89%) bins.
"""

Any ideas?
Thank you
Best,
Alla

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