Ethanol oxidation present in MW-score but missing from draw carbon cycle figures

[lacy111693]

Hello, looking at the MW-score result text file, I noticed the MW-score for each function specific to ethanol oxidation is 5.3 (for my particular data) but it is missing in the draw_carbon_cycle_total figure (it shows 0 genomes and 0% coverage). I went to look at the individual carbon cycle figures for each of my MAGs, and it seems to be missing on those too. The MW-score shows its present in all of my phyla though. When I ran METABOLIC-C with the genus flag, ethanol oxidation is missing in exactly half of my genera but present in the other half, so it definitely should not show 0 genomes in the cycle figure. Thoughts?

A secondary question, I have some other pathways showing 0 genomes and 0% coverage in cycle figures. When I went to double check those in the MW-score result, they are outright missing from the table. It doesn't show zero, they just aren't there. Should they be there and have a zero value? Or is that normal and they are simply excluded from the mw-score result if its a zero value?

ethanol oxidation should be present here:

Phyla level mw-score

Genus level mw-score (its not showing all of the columns)

[lacy111693]

@patriciatran so sorry to bother you again! Do you have any insight for this?

[lacy111693]

For anyone having this issue, I think I've found the fix. The R_pathways.txt file is what is used to draw the biogeochemical cycles. The MW-score_reaction_table.txt is used for the MW-score. For some reason with ethanol oxidation in these files, R_pathways only looks for one gene (K00001.hmm) but MW-score_reaction_table looks for multiple (K00129.hmm,K00138.hmm,K13954.hmm,K00001.hmm,K04072.hmm,K00114.hmm,K00002.hmm,K04022.hmm,K22473.hmm).

So this is why I was seeing ethanol oxidation in the mw-score but not the drawn cycles. I added all the genes that the MW-score table looks for into the R_pathways file on my computer and now the cycles are drawing as I'd expect.