Output visualizations - alpha/beta diversity analysis

[cdl]

Hi!
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!
Celia

[cdl]

I just noted when exporting bray_curtis_pcoa_results to .txt that the D1-T0 sample is missing...

qiime tools export --input-path bray_curtis_pcoa_results.qza --output-path bray_curtis_pcoa_results.txt

ordination.txt (3.9 KB)

[thermokarst]

Hello @cdl!

@cdl

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)

According to the provenance in jaccard_emperor.qzv, you applied a filtering step before generating the core-metrics results, but then for the files in the second half of your post, you did not apply that filtering step. My guess is that you have a) mixed up your input files, since it seems like you are working with two parallel workflows and b) have likely filtered that sample out (maybe on accident?).

Hope that helps!

[cdl]

Thank you a lot for the prompt reply! I started from the beginning again and it works now. I guess I mixed up the input files.