I am using qiime2-2019.10 in conda environment.
I have a total of 14 samples to perform diversity analysis. My code runs fine and I obtain the core-metrics-results directory with the associated metrics. (I employed a sample depth of 97420 since this is the smaller count across my samples).
# Alpha and beta diversity analysis
qiime diversity core-metrics-phylogenetic --i-phylogeny rooted-tree.qza --i-table feature-table-filtered.qza --p-sampling-depth 97420 --m-metadata-file metadata.tsv --output-dir core-metrics-results
The problem is that I am missing one sample (D1-T0) in the output visualizations:bray_curtis_emperor.qzv (803.9 KB) jaccard_emperor.qzv (803.9 KB) unweighted_unifrac_emperor.qzv (804.3 KB) weighted_unifrac_emperor.qzv (804.3 KB)
However, in the corresponding pcoa-results.qza the missing sample (D1-T0) appears.bray_curtis_pcoa_results.qzv (1.2 MB) jaccard_pcoa_results.qzv (1.2 MB) unweighted_unifrac_pcoa_results.qzv (1.2 MB) weighted_unifrac_pcoa_results.qzv (1.2 MB)
Note that the missing sample is the one employed to set the --p-sampling-depth. Maybe this has something to do with the issue, I am not sure.
How can I solve this?
Thanks a lot in advance!