When running gene_mapping and enabling biomart it will always throw the warning biomart query failed.
Apparently, it expects a non-html file (more like a tsv) as a response, but currently biomart seems to return an html. Status code is 200 nonetheless.
How to reproduce the issue?
Create a run that uses the gene mapping step and make sure to check the box Use Biomart after Uniprot databases (online). [It probably needs some kind of previous step, but I'm not sure what it needs.]
What is the expected behavior?
Getting the actual response from biomart, which you would get when sending a correctly formatted query
What is the issue?
When running
gene_mappingand enabling biomart it will always throw the warningbiomart query failed.Apparently, it expects a non-html file (more like a tsv) as a response, but currently biomart seems to return an html. Status code is 200 nonetheless.
How to reproduce the issue?
Create a run that uses the gene mapping step and make sure to check the box
Use Biomart after Uniprot databases (online). [It probably needs some kind of previous step, but I'm not sure what it needs.]What is the expected behavior?
Getting the actual response from biomart, which you would get when sending a correctly formatted query