I was running through the gneiss tutorial today with a toy dataset of my own. It turns out that some of the sample IDs in my metadata table didn’t match the sample IDs in my feature table. The non-overlapping samples were filtered during the gneiss tutorial workflow, but as far as I can tell, there was no warning that some samples had been filtered out. I just noticed after carefully examining the output of qiime gneiss dendrogram-heatmap.
This behavior of filtering samples (& features?) without warnings is really dangerous, given that someone could easily conduct an analysis in qiime without realizing that some samples were accidentally removed. It would be really helpful to have a warning stating that some samples/features have been filtered and a list written to a log file in /tmp/
Maybe this has been fixed in the most recent version (we’re holding out on updating due to the conda install issues).
$ qiime info
System versions
Python version: 3.5.4
QIIME 2 release: 2017.10
QIIME 2 version: 2017.10.0
q2cli version: 2017.10.0
Installed plugins
alignment 2017.10.0
composition 2017.10.0
dada2 2017.10.0
deblur 2017.10.0
demux 2017.10.0
diversity 2017.10.0
emperor 2017.10.0
feature-classifier 2017.10.0
feature-table 2017.10.0
gneiss 2017.10.0
longitudinal 2017.10.0
metadata 2017.10.0
phylogeny 2017.10.0
quality-control 2017.10.0
quality-filter 2017.10.0
sample-classifier 2017.10.0
taxa 2017.10.0
types 2017.10.0
vsearch 2017.10.0