Output of prioritization workflow

Microbial community profiling MetaWIBELE
1

Hi,yancong,
It took me some time to finally install the software completely. The characterization workflow has been successfully tested, but why is the prioritization workflow lacking supervised results?
it’s my output result from prioritization workflow

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my command is metawibele prioritize --prioritization-config prioritization.cfg --input-annotation demo_proteinfamilies_annotation.tsv --input-attribute demo_proteinfamilies_annotation.attribute.tsv --output Output_priorization

and the prioritization.cfg is displayed as follows:

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Thanks,mona.

2

Hi Mona,

Did you customize the phenotype parameter in your metawibele.cfg file? You need to specify the phenotype parameter with the main phenotype metadata of interest (e.g. disease_diganosis) for supervised prioritization. MetaWIBELE will skip supervised prioritization if phenotype = none. More guidance about the parameter setting of metawibele.cfg is shown in GitHub - biobakery/metawibele: MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome.

Thanks!
Yancong

3

Oh, I get it. Thanks a million. But does the phenotype parameter influence the results from the characterization workflow?

4

Yes, if you customize the phenotype parameter, MetaWIBELE will process association analysis in the MetaWIBELE-characterize step and format the association results into another type of annotation in the characterization outputs. These association results will be used for supervised prioritization in the MetaWIBELE-prioritize step.

Thanks!
Yancong