Hi Qiime2 team!
First of all, I would like to thank the possibility to view qiime2 workshop last week. It was very good and helpful for me (2-month-old q2 user).
I have a question about an error in the plugin qiime diversity core-metrics-phylogenetic. After conducting taxonomic classification with a trained SILVA138 for V3-V4 region, I wanted to filtered out mitochondrial and chloroplast sequences. These were the commands:
$qiime taxa filter-seqs
$qiime feature-classifier classify-sklearn
–o-classification taxonomySIL_MC.qza \
$qiime taxa filter-table
–o-filtered-table table_MC.qza \
Until here there were no problem. With the new table, I could check alpha-rarefaction and phylogeny, as follows:
$qiime diversity alpha-rarefaction
–p-max-depth 15000 \
$qiime phylogeny align-to-tree-mafft-fasttree
The problem is in the following command:
$qiime diversity core-metrics-phylogenetic
–output-dir ./core-metrics-results_MC \
The error is:
Plugin error from diversity:
The table does not appear to be completely represented by the phylogeny.
Please help me qiime2 experts!
Thanks a lot!