When doing the Alpha and Beta divergence analysis, I use the commands described in qiime2:
qiime feature-table summarize
--i-table table.qza
--o-visualization table.qzv --m-sample-metadata
--m-sample-metadata-file sample-metadata.tsv
qiime feature-table tabulate-seqs \ --i-data rep-seqs
--i-data rep-seqs.qza
--o-visualization rep-seqs.qzv
Using as sample-metadata.tsv the data file that comes out when you visualize the able.qzv. But I'm getting an error and I don't know if it's because of this metadata step that I'm using the wrong one. It says this:
Plugin error from diversity:
Ordinations with less than two dimensions are not supported.
Debug info has been saved to /var/folders/gk/q2nm38xd67l_c4r76vz0tz8m0000gn/T/qiime2-q2cli-err-f68u2rhx.log
What do you think is going on and how can I solve it?
Hi!
Looks like you are trying to calculate diversity metrics with a table that contains only one sample. If you are sure that you have more than 1 sample, make sure that while calculating diversity metrics you set appropriate sampling depth value. Too high sampling depth may lead to most of your samples be filtered out from the table during rarefaction. Just check your table.qzv and compare number of reads there per sample to sampling depth you set in the command.
Yes, I was using only one sample and adding more samples solved the error. Now I have problems in the next step with the metadata. I attach my table, do you see where the error could be?
For metadata erros, please check this tutorial. Validation through google sheets and keemei works very well and it can point out on any errors that can escape human eye.
I have run it through Keemei and it has validated it, however I still get the same error when I put this command: metadata_3.tsv (761 Bytes)
(qiime2-2023.2) vanesa@MacBook-Pro-de-Vanesa emp-paired-end-sequences % qiime diversity alpha-group-significance
--i-alpha-diversity core-metrics-results/faith_pd_vector.qza \
--m-metadata-file metadata_3.tsv \
--o-visualization core-metrics-results/faith-pd-group-significance.qzv
Metadata does not contain any columns that satisfy this visualizer's requirements. There must be at least one metadata column that contains categorical data, isn't empty, doesn't consist of unique values, and doesn't consist of exactly one value.
Debug info has been saved to /var/folders/gk/q2nm38xd67l_c4r76vz0tz8m0000gn/T/qiime2-q2cli-err-bxc23c8c.log
Plugin error from diversity:
Metadata does not contain any columns that satisfy this visualizer's requirements. There must be at least one metadata column that contains categorical data, isn't empty, doesn't consist of unique values, and doesn't consist of exactly one value.
Debug info has been saved to /var/folders/gk/q2nm38xd67l_c4r76vz0tz8m0000gn/T/qiime2-q2cli-err-d78bxryg.log
