The following error has been encoutered while running the qiime sample-classifier classify-samples.
I have around 167 samples - the metadata column given for classifer is "subject"- which actually contain 85 healthy and 82 Diseased samples (screenshot of metadata attached just for a clarity).
I have used the same command for another public dataset and it seems to be working perfectly.
Could you please help me out to solve this issue.
Plugin error from sample-classifier:
Linkage must be computed on at least two observations.
qiime sample-classifier classify-samples
Thanks for reaching out, and for providing those details! I'd like to call out this error message from what you provided above:
This message indicates that there is only one class within your data, and
sample-classifier needs at least two in order to proceed. Another good example of this error with additional details can be found in this forum post, for reference.
Actually I am using the column "subject" from my metadata file.
Under subject I have two different classes namely "healthy" & "diseased".
I have already attached the screen shot of the same in my previous post.
Hope you meant the same by saying "class"
Happy to clarify - put another way, there is only one observation (or sample) that is being found within the data.
You should check out the input table to make sure everything looks as you expect it to, and check your parameter settings to make sure (as an example) that you are not collapsing your entire table into one sample based on some metadata value.
If you haven't taken a look at the forum post I linked in my previous response, I'd highly recommend it - this discusses a couple more troubleshooting steps that you can take on your end when running into this error.
Thanks Lizgehret !
I will go through the forum and do check on with my feature and metadata table.
To add on - I have many samples in my dataset too.
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