Hi User support,
I looked through the forum and could not find an answer for my error, so I hope I did not miss it.
I am trying to run qiime longitudinal pairwise difference comparisons on a feature table to see whether there are specific taxa that change across time.
I use qiime2-2019.10 on an ubuntu machine.
This is the command I used:
qiime longitudinal pairwise-differences --i-table cleaned-L2-rel.qza --m-metadata-file map.txt --p-metric k__Bacteria;p__Actinobacteria --p-group-column Diet --p-state-column Time --p-state-1 1 --p-state-2 3 --p-individual-id-column Pt --p-replicate-handling random --o-visualization pairwise-differences-actino.qzv
This is the error I got:
There were some problems with the command:
(1/5) Missing option “–p-state-column”.
(2/5) Missing option “–p-state-1”.
(3/5) Missing option “–p-state-2”.
(4/5) Missing option “–p-individual-id-column”.
(5/5) Missing option “–o-visualization”. ("–output-dir" may also be used)
p__Actinobacteria: command not found
So I thought that the “;” in k__Bacteria;p__Actinobacteria was creating problems and I tried running this:
qiime longitudinal pairwise-differences --i-table cleaned-L2-rel.qza --m-metadata-file map.txt --p-metric p__Actinobacteria --p-group-column Diet --p-state-column Time --p-state-1 1 --p-state-2 3 --p-individual-id-column Pt --p-replicate-handling random --o-visualization pairwise-differences-Actino.qzv
Plugin error from longitudinal:
metric must be a valid metadata or feature table column.
It seems that like this is not recognizing the feature either. I am sure this is probably a very silly problem but I can’t figure it out, hope you understand where the error is!
Thank you very much
Giada