Are bin_compare and bin_qa_plot functions still working?

[snehamurthy21]

Hello,

I was trying to compare bins across different algorithms and came across this functions bin_compare and bin_qa_plot under checkm, but both seem to no longer work? is it removed? or am i doing something wrong.

_### checkm bin_compare 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: argument subparser_name: invalid choice: 'bin_compare' (choose from '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')_

[ElsaMMendes]

Hey, I was looking for bin_qa_plot also. Both bin_compare and bin_qa_plot have been removed: https://github.com/Ecogenomics/CheckM#removed-functionality

[snehamurthy21]

Oh Thank you! It seemed very useful command, seen the plot in many papers

Do you know of any alternative tools or command for same?

[ElsaMMendes]

If you have a lot of bins maybe you should skip the figure.... because with too much bins it's a bit complicated. You can still check the log to have the informations (the log should have a table with this header):

Or you can check the code of bin_qa_plot to get inspired to lunch it on your own. Or you can use a tool called " METAWRAP" (also check version, I have version 1.2), when you install it with conda, you have access to several tools. you have access to the previous version of checkM (with the lost functions such as bin_qa_plot).

[snehamurthy21]

Thank you @ElsaMMendes