I build the rooted-tree.qza according to the tutorial, and then calculate the core diversity, but when I open core metrics results / bray_ curtis_ distance_ matrix.qza I found that the distance between groups was 1. I think there is something wrong with this result, but I don't know where the error is.
Are you just following along with a tutorial, or are you using your own data? Either way, which tutorial are you looking at? Please share the exact commands you ran to up until this point.
I used my own data and the running process referred to the mouse tutorial. My data is paired and import in manifest file format.
First, I ran the command:
time qiime dada2 denoise-paired --i-demultiplexed-seqs demux.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 275 --p-trunc-len-r 205 --o-table table.qza --o-representative-sequences dada2-rep- seqs.qza --o-denoising-stats stats.qza --p-n-threads 0
And then I run the command to build the system development tree:
time qiime phylogeny align-to-tree-mafft-fasttree --i-sequences dada2-rep-seqs.qza --o-alignment aligned-rep-seqs.qza --o-masked-alignment masked-aligned-rep-seqs.qza --o-tree unrooted-tree.qza --o-rooted-tree rooted-tree.qza
Finally, I ran the following command to calculate the core diversity:
time qiime diversity core-metrics-phylogenetic --i-phylogeny rooted-tree.qza --i-table table.qza --p-sampling-depth 6900 --m-metadata-file metadata.txt --output-dir core-metrics-results
So I got bray_ curtis distance matrix, but found that the distance between groups is 1. I think this is abnormal. In addition, I also found that table.txt In the file, each OTU appears only once in a sample group, which is also abnormal.
I don’t know why this problem appears and I can’t solve it. It bothers me.
This is the content displayed in the feature table file that I exported from qiime2. Each OTU appears only once in one sample, which is incorrect.
Are you able to share the visualizations generated by
qiime metadata tabulate and
qiime feature-table summarize? You can send them to me in a DM if you’d like.
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