Is it possible to have the species level MN-score_results.txt?

[B-1991-ing]

Dear METABOLIC support team,

Is it possible for me to generate the species level MN-score_results.txt based on the METABOLIC-C.pl command line below? The I want to plot the species level MN-score_results.txt as the example phyla level plot. As now, I only have 55 species MAGs.

The METABOLIC-C.pl command line perl /services/tools/metabolic/4.0/METABOLIC/METABOLIC-C.pl -in-gn ${metabolic_c_dRep95_comp70_con5_fasta} -r ${trimmed_paried_reads_location1} -o ${metabolic_c_dRep95_comp70_con5_outdir} -t 32

Best,

Bing

[B-1991-ing]

Dear METABOLIC support team,

Update After reading the similar question - Metabolic network diagrams #26, I downloaded the perl scripts - METABOLIC-C.pl and METABOLIC-C.2nd_run.pl. Added the parameters needed to run the METABOLIC-C.2nd_run.pl as shown below.

perl /services/tools/metabolic/4.0/METABOLIC/METABOLIC-C.2nd_run.pl -in-gn ${path_to_folder_with_genome_files_of_a_previous_run} -r ${path_to_list_of_paired_reads} -o ${output_directory_of_a_previous_run} -2nd-run true -2nd-run-suffix MW_scoretaxgenus -depth-file All_gene_collections_mapped.depth.txt -tax genus -t 32

But, according to the scripts - METABOLIC-C.pl and METABOLIC-C.2nd_run.pl, there are only at genus level instead of "species" level.

Best,

Bing

[ChaoLab]

I have just updated the scripts to include "species" level

[B-1991-ing]

Thank you so much, I will have a try later.

[B-1991-ing]

So, the version is not updated, we just need to reinstall the current METABOLIC 4.0?

[ChaoLab]

Yes, the version keeps the same