I am doing a meta-analysis with multiple different studies. I have a very strong study effect occurring on my data, making the PCoA plots look like "Y"s because it is so strong. Speaking with another person, they suggested that I collapse to the phylum level to remove the strong differences. However, I am encountering an error when I try to run the core-metrics after I collapse the table. Below is the example:
qiime taxa collapse
qiime diversity core-metrics-phylogenetic
The error message is as follows:
Plugin error from diversity:
feature_ids must be present as tip names in
feature_ids not corresponding to tip names (n=21): k__Bacteria;p__Cyanobacteria k__Bacteria;p__Bacteroidetes k__Bacteria;p__Planctomycetes k__Bacteria;p__Fibrobacteres k__Bacteria;p__Deferribacteres k__Bacteria;p__Verrucomicrobia k__Bacteria;p__Synergistetes k__Bacteria;__ k__Bacteria;p__OD1 k__Bacteria;p__Proteobacteria k__Bacteria;p__Tenericutes Unassigned;__ k__Bacteria;p__WPS-2 k__Bacteria;p__Fusobacteria k__Bacteria;p__Firmicutes k__Bacteria;p__Lentisphaerae k__Bacteria;p__Actinobacteria k__Bacteria;p__ k__Bacteria;p__Elusimicrobia k__Bacteria;p__Spirochaetes k__Bacteria;p__TM7
I checked the table, and I couldn’t find the labels, because there was a space in-between the kingdom and phylum like this: “k__Bacteria; p__TM7” (vs this “k__Bacteria;p__TM7”).
I think that might be why the error is occurring. I tried removing the spaces, but then the file was never in the correct format to use again.