Good morning
I'm trying to perform longitudinal analysis on my data but I have an error.
The code that I used:
qiime longitudinal pairwise-differences
--m-metadata-file metadata_formula_milk.tsv
--m-metadata-file shannon_vector.qza
--p-metric shannon
--p-group-column Diet
--p-state-column Time
--p-state-1 0
--p-state-2 1
--p-individual-id-column StudyID
--p-replicate-handling random
--o-visualization shannon_dif_formula.qzv
metadata_formula_milk.tsv (1.8 KB)
message error:
Plugin error from longitudinal:
metric must be a valid metadata or feature table column.
I can't understand my error.
Can someone help me??
Thanks
timanix
(Timur Yergaliyev)
October 7, 2020, 10:02am
2
rparadiso:
–p-metric shannon
Hi!
Are you running the last vesrion of Qiime?
If yes, replace this parameter to
--p-metric shannon_entropy
They renamed a column in the artifact
1 Like
rparadiso
(Rubina)
October 7, 2020, 10:55am
3
Thanks @timanix the problem was exactly that, also other metrics have changed? Where can I check?
timanix
(Timur Yergaliyev)
October 7, 2020, 11:00am
4
Yeah, some of them. You can open a .qza file as an archive or export it, open data subdirectory and check column names.
evenness now pielou_evenness
and observed_otus - observed_features
2 Likes
rparadiso:
Where can I check?
Another convenient way (without exporting!) is to use qiime metadata tabulate
and this will allow you to visualize/search the results.
2 Likes
system
(system)
Closed
November 7, 2020, 5:37pm
6
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