Hi
I have a problem while analyzing alpha rarefaction.
I tried to extract the alpha rarefaction plot based on the phylogenetic tree.
Analysis process is as follows.
First, I made a table for the genus level.
command : qiime taxa collapse --i-table table.qza --i-taxonomy taxonomy.qza --p-level 6 --o-collapsed-table table-collapsed-L6.qza
Second was to input pylogenetic tree and the table from which the genus level was extracted.
Command: qiime diversity alpha-rarefaction --i-table table-collapsed-L6.qza --i-phylogeny rooted-tree.qza --p-max-depth 74250 --m-metadata-file sample-metadata.tsv --p-metrics observed_otus --p-metrics shannon --p-metrics faith_pd --p-metrics pielou_e --o-visualization alpha-rarefaction.qzv
The following error occurred
Error: Plugin error from diversity:
All feature_ids must be present as tip names in phylogeny. feature_ids not corresponding to tip names (n=17):
D_0__Bacteria;D_1__Actinobacteria;D_2__Actinobacteria;D_3__Micrococcales;D_4__Brevibacteriaceae;D_5__Brevibacterium
D_0__Bacteria;D_1__Actinobacteria;D_2__Acidimicrobiia;D_3__uncultured;;
D_0__Bacteria;D_1__Actinobacteria;D_2__Actinobacteria;D_3__Micrococcales;D_4__Micrococcaceae;__
D_0__Bacteria;D_1__Bacteroidetes;D_2__Bacteroidia;D_3__Bacteroidales;D_4__Prevotellaceae;D_5__Prevotella 6
D_0__Bacteria;D_1__Actinobacteria;D_2__Actinobacteria;D_3__Micrococcales;D_4__Dermacoccaceae;D_5__Dermacoccus
D_0__Bacteria;D_1__Actinobacteria;D_2__Actinobacteria;D_3__Micrococcales;D_4__Micrococcaceae;D_5__Micrococcus
D_0__Bacteria;D_1__Actinobacteria;D_2__Actinobacteria;D_3__Micrococcales;D_4__Dermacoccaceae;D_5__Kytococcus ...
How do I fix this error?
Or is there any other way to draw a specific taxon level's rarefaction plot?
Attached is table.qza, taxonomy.qza, table-collapsed-L6.qza, rooted-tree.qza.
rooted-tree.qza (222.6 KB) table.qza (209.0 KB) table-collapsed-L6.qza (102.5 KB) taxonomy.qza (296.7 KB)
I'd appreciate your help.