jwdebelius
October 19, 2020, 9:42am
3
Hi @lilycrook ,
The error says there are tips in your tree that aren't in your feature table. This has been an issue before. Please check out some of the previous posts.
Hi,
I am a beginner of qiime2, and please let me know your advise.
I want to analyze my Sanger sequenced data by qiime 2 pipeline.
After I imported a combined fasta file which was made by the command, "add_qiime_labels.py" under qiime1 environment, I commanded "vsearch" for dereplicating/clustering with qiime2.
Using rep-seqs.qza and table.qza, I carried out generating .a tree for phylogenic analyses(aligned-rep-seqs.qza, masked-aligned-rep-seqs.qza, unrooted-tree.qza, rooted-tree.qza).
Wh…
Hey @laibinhuang !
Let's take a closer look at the IDs in both of those Artifacts you have shared:
import qiime2
import skbio
import biom
tree = qiime2.Artifact.load('EAA_AamoA_rootedtree.qza').view(skbio.TreeNode)
table = qiime2.Artifact.load('EAA_AamoAtable.qza').view(biom.Table)
tree_ids = {t.name for t in tree.tips()}
table_ids = set(table.ids(axis='observation'))
Then, if I print out the tree IDs:
print(tree_ids)
{'0048d0d890fb577f2bb2970047f0418734ac8df3 site4_AamoA_H03',
'0291c9f44…
Best,
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