What should I do for it smooth operation?

[Catherine]

Alpha Group Significance Error

Hi there @bye_ology! This method is all about regrouping samples into categories relevant to your study - control vs treatment, before/after intervention, etc. What that error is saying is that none of your metadata values were able to create groups with more than sample in it. Yikes, that is super low, but isn’t the issue here (also, you could rarefy at 63, which would keep the same samples, but would buy you a little more depth…). Can you provide a sample of your metadata file? Thanks! …

Hello thermokarst,I have the same problem,but there are still some difference and I need your help.Firstly,I just use two samples (C1,C2) for example.Secondly,I use qiime2-2018.6 version.Thirdly,the codes I use are as follows:qiime diversity alpha-group-significance --i-alpha-diversity core-metrics-phylogenetic/faith_pd_vector.qza --m-metadata-file sample-metadata.tsv --o-visualization core-metrics-phylogenetic/faith-pd-group-significance.qzv
So what should I do for it smooth operation?

[thermokarst]

Hey there @Catherine - can you please copy-and-paste the error message you are observing? As well, can you please provide your metadata? Thanks!

PS - it looks like you might've accidentally sent this original question to me in a private message - I moved it out here to the forum so that others can benefit from searching our discussion. Thanks!

[Catherine]

Thanks，you are very thoughtful,the last question has been solved,now this question:after input codes: qiime diversity alpha-group-significance --i-alpha-diversity core-metrics-phylogenetic/faith_pd_vector.qza --m-metadata-file sample-metadata.tsv --o-visualization core-metrics-phylogenetic/faith-pd-group-significance.qzv,the error messages like this: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.
I use qiime2-2018.8 version to analyze two samples and the metadata is as follows:
Thank you for your kindly reply again.

[thermokarst]

Hey there @Catherine!

So, according to the error, the following criteria must be satisfied by your metadata in order to compute these plots:

1. There must be at least one metadata column that contains categorical data AND
2. That metadata column can't be empty AND
3. That metadata column doesn’t consist of unique values AND
4. That metadata column doesn’t consist of exactly one value.

Okay, so, let's break it down in terms of the metadata you have shared with us:

• BodySite: this doesn't pass the test, because all of the values are identical (rule 4)
• Subject: this doesn't pass the test, because all of the values are identical (rule 4)
• Description: this doesn't pass the test, because all of the values are identical (rule 4)
• Group: this doesn't pass the test, because all of the values are unique (rule 3)

Does that make sense? For all of those metadata columns there really isn't anything to plot - there would either be one group, or, all of the groups would represent only one sample.

Moreover, technically it is impossible to satisfy those criteria with only two samples --- you will need more than that to perform any kind of meaningful comparison.