Bacteroides vulgatus CAG:6 becomes Bacteroides.vulgatus.CAG.6 when loaded as snakemake inputs, causing error in df.loc
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sherlyn99 commented
Got a KeyValueError of 'Bacteroides.vulgatus.CAG.6' at here whereas the original OTU ID in feature_table.tsv is 'Bacteroides vulgatus CAG:6'
not sure the exact reason but a quick fix is to substitute all space and :'s in the OTU IDs in feature_table.tsv to . and then convert the feature table to .biom using biom-convert
yangchen2 commented
I am encountering this pattern of errors as well. I believe it has to do with Maaslin2: https://forum.biobakery.org/t/maaslin2-changes-the-feature-names/5525 Working on a fix for this now.