Metacyc pwy regroup option missing?

Microbial community profiling HUMAnN
1

Hi,
I’m trying to assign Metacyc Pathway IDs to my humann3 data.

However, I can’t see the “metacyc-pwy” group option under the humann_regroup_table option. I know rxn=metacyc-rxn but it seems this is not compatible with metacyc-pwy rename command.

Thanks

2

Nm someone else has explained that the default output is Metacyc and so there is no need to regroup before using the rename to Metacyc-PWY function.

However, (and this is probably why I thought there was a missing step earlier) when I run the rename for metacyc-pwy I get no output:
“Renamed 0 of 1575751 entries (0.00%)”

Any sugestions?

3

Hi @emihoe,
could you provide the humann command you ran and the log that was output ? That might help us figuring out what’s going on.

4

Agreed that this additional info will help. Pathways should be named by default in the HUMAnN output.

5

Sorry for excluding that

humann -i sample1_cat.fastq.gz --threads 48 -o sample1_humann_out/

humann_join_tables -i uniref90/ -o All_genefamilies.tsv --file_name genefamilies

humann_renorm_table -i All_genefamilies.tsv -o All_genefamilies.tsv-rel.tsv -u relab

##regroup based on diff databases, metacyc (=rxn), KO, EC, PFam
humann_regroup_table --input All_genefamilies.tsv-rel.tsv \ –groups uniref90_pfam --output All_genefamilies.tsv-rel_pfam.tsv

##rename based on the regroup selection

Here is where I got confused as one of the options for -n is metacyc-pwy
Using -n metacyc-pwy with any of the regroup files or the output from humann_renorm_table = “Renamed 0 of 1575751 entries (0.00%)”

humann_rename_table -i genefamilies_rel_ko.tsv -o genefamilies_rel_ko_named.tsv -n kegg-orthology

I spoke with someone else and they pointed out that the original output from the humann pipeline has the metacyc-pwy at the bottom of the output.

Have I understood this correctly? That the humann_renorm_table -n metacyc-pwy is a red herring?

Thank you for the help!

6

One of the main outputs of HUMAnN is the pathway abundance table (getting to this table from genes is a two-step process, hence we do it for you automatically rather than relying on the simpler one-step regroup script). The pathways in that file have already been named using the pathway-name mapping file that the rename script can see. In theory if you had stripped the names off of the pathways (leaving only the IDs) you could use the rename script to reattach them (but that would be an unusual situation).