I've run my sequences through the Qiime2 pipeline and have reached the point of calculating alpha and beta diversity metrics for my data. However, when I try and run beta diversity I get the following error: Plugin error from diversity:
Ordinations with less than two dimensions are not supported.
Debug info has been saved to /tmp/qiime2-q2cli-err-l2dzwpsf.log
This error resulted from the following code: "qiime diversity core-metrics-phylogenetic --i-phylogeny rooted-tree.qza --i-table table.qza --p-sampling-depth 4868 --m-metadata-file Plate001_Qiime.tsv --output-dir core-metrics-results"
I'm assuming that the issue is arising from an insufficient mapping file? I'm currently using just my manifest file, which I show below:
Could I fix the problem and calculate my diversity matrices by adding columns for other variables (year, sampling depth, etc?) Or are there other issues leading to this error?
Thanks for your help! I'm hoping that I'm close to running my first dataset through Qiime2.
The problem doesn't actually have to do with your mapping file. It's a little bit confusing, but what it's actually telling you is that your distance matrix only has 2 samples. For every pairwise distance in your matrix, you get a new dimension in your ordination. At your current depth, samples aren't surviving.
You might check your feature table summary to see if your depth is appropriate. It looks like you picked the depth of the shallowest sample (I'm guessing). You could also try rarifying the table (
qiime feature-table rarefy - double check my spelling with the help docs) to make sure the full table is surviving.
Metadata wise, I would recommend avoiding spaces. A lot of the tools don't play nicely with spaces; you already have a dash character ("-"). It could be that the spaces are messing with the distance matrix/ordination representation that sits under QIIME 2, but that doesn't explain why there would only be 1 sample remaining.
Thanks for this! It turns out the issue was earlier on in the pipeline, where trunc-r & f values were set too high!
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