Hi,
Fresh user here. This is my first time trying out QIIME2. I have been analyzing a single .fastq file from 16S Iontorrent sequencing. I had good luck with demux and denoising, but I got an error message whenever I get to Qiime diversity core-metrics phylogeny. The error message reads out as Plugin error from diversity: Ordinations with less than two dimensions are not supported. I am not entirely sure where I am going wrong. I have checked my metadata with keemei too. Please suggest what else can I do to circumvent this error.
If you're processing one sample, you can't do ordination because you can't calculate a distance past the sample and itself.. which then makes it hard to project into ordination space because there's only one dimension. (There's some magic with ordinations pace where you twist the distances to maximize visual separation... its hard to twist with only one distance, especially when that distance is 0.)
My best recomendation is to work through either a sequencing run (if you have multiple) to get a table, or just work with all your data, unless you're really computationally limited. There are always delightful, funny things that come up in a full dataset that are hard to anticipate off a single sample.
If you're worried about processing power, the major places people have issues are (1) denoising with DADA2, (2) training feature classifiers and (3) Diversity calculations on large datasets. But, once you have a feature table, diversity calculations, and taxonomic classifications, you can handle thousands of samples on a laptop.
I have successfully reached Phylogenetic tree construction step and obtained rooted and unrooted qza files. The next step involves making core-metrics directory which is giving me an error. Please let me know what changes should I do in my commands? or any other way to resolve this issue?
Okay, that's one option down. Could you use use qiime diversity beta to try and calculate a distance matrix (if one hasn't come out of the pipeline already)? Would you be willing to share the distance matrix?
@jwdebelius There are no type of core metrices that are being generated. I have reached only rooted/unrooted tree part. The further part is not getting executed.
Okay, then you'll need to rarify your table using qiime feature-table rarefy with --p-sampling-depth 4340. Please summarize that feature table with qiime feature-table summarize and share the sample counts.
Then, use qiime diversity beta to generate a distance matrix, maybe with Jaccard or Bray-Curtis. Would you be willing to share those results here?
