I’m trying to run alpha and beta diversity analyses with data I’ve downloaded from Qiita and
I’m receiving a pluggin error. I converted qiime artifacts into .qza files following this tutorial. I’m running QIIME2 version 2018.11 and installed it using conda.
Here is the command I’m trying to run:
This error means that the samples that are present in your biom table are not all located on your phylogenetic tree. Can you tell me where you got your table.qza from (is it from closed reference OTU table, deblur reference hit table, or deblur final hit table) and which rooted-tree.qza you’re using (if it’s from the closed reference OTU table is it: greengenes, SILVA, UNITE or is it from the deblur reference hit table)?
So you will have to filter your table.qza based on your tree.qza (basically removing any OTUs that aren’t present on your tree). There are 3 ways to do this.
On Qiita, go to create analysis and create an analysis using your deblur reference hit table. Download the biom table from your first analysis artifact instead of the one located on the deblur reference table on the study page. When you create an analysis from the deblur reference-hit table, it automatically removes the OTUs that are not located on the phylogenetic tree so you don’t have to do it.
You can follow the steps listed in the tutorial you referred to that were written prior to the qiime fragment-insertion filter-feature command being included in the core QIIME2 commands. Run the following commands:
echo “feature-id” > qiita-files/sepp-tips.txt
python -c “from skbio.tree import TreeNode; print(’\n’.join([tip.name
for tip in
TreeNode.read(‘qiita-files/insertion_tree.relabelled.fix.tre’).tips()
if not tip.name.isdigit()]))” >> qiita-files/sepp-tips.txt