May I receive insight into taxonomy labeling for phylogenetic trees? I processed my metadata, ASV table, and phylogenetic tree through QIIME2 then uploaded those files into MBanalyst. Everything uploaded fine, however when running phylogenetic analysis (such as Unifrac) I receive the error ‘Tree tip labels do not match feature names in the OTU/taxonomic tables!’. Since I ran everything through the DADA2 pipeline I’m not sure where the discrepancy is or how to fix it.
Hello，
Could you please update your post based on our response to this question ?
That will be helpful for checking the problems.
You can share the files necessary for reproducing the error online or by email to yao.lu5@mail.mcgill.ca.
Thanks,
Yao
Okay I am so close to getting this phylogenetic tree to work, but am missing one final step. I fixed the ‘tree tips labels do not match feature names in the OTU/taxonomic tables!’ error by creating an ASV and taxonomy ID table from my feature table from the QIIME2 dada2 pipeline at the denoising step. After filtering for chloroplast and mitochondria, I was able to use the biom file to connect the ASV IDs to the tree tip labels. From here, a taxonomy ID tabel will link your ASV IDS to bacteria taxonomic names you want to see in Microbiome Analyst.
However, this is where I am stuck. If I just upload the metadata with the ASV IDs and tree file, I can get beta diversity but everything is labeled with ASV IDs instead of the taxonomic names.
If I try to upload the metadata, ASV IDs, tree file, and taxonomy file then I get the ‘tree tips do not match’ code again.
Help to fix this last discrepancy would be much appreciated.
Tool & Module Used: Microbiome Analyst->marker data profiling option to upload data->using all fields to upload ASV table, metadata, taxonomy file, and tree.
I converted my feature table into a biome table using the code below to be able to match ASV ID’s in my phylogenetic tree.
qiime tools export
–input-path dada2_table-no-mitochondria-no-chloroplast_FECAL_single.qza
–output-path feature-table_FECAL_single_notmito_nochlor
biom convert
–input-fp feature-table_FECAL_single_notmito_nochlor/feature-table.biom
–output-fp feature-table_FECAL_single_notmito_nochlor/feature-table_FECAL_single_notmito_nochlor.txt
–to-tsv
Using just this ASV file I can get beta diversity using my tree file, but the identifying information is a series of numbers and letters instead of taxonomic identification.
To get around this I then used the code below to link the ASV IDs to taxonomy.
qiime metadata tabulate
–m-input-file taxonomy_silva_FECAL_single.qza
–o-visualization taxonomy_silva_FECAL_single.qzv
However, when I upload the metadata, ASV, taxonomy, and tree files all together I get a ‘tree tips do not match’ error code. I have those exact files attached to this post except for the tree file as it is too large.
Yao I did send an email request with all the files if you would be so kind to look them over. I will post here with the resolution once we come to a conclusion.
ASV Table_FECAL_single_notmito_nochlor.txt (1.8 MB)
fasting_2022_FECALmetadata_ControlsRemoved.txt (13.7 KB)
FECAL_Taxonomy_Table_For_MBanalyst.txt (404.6 KB)
Hello, as the tree file was not provided here, I would like to make sure if your tree file was in the right format as we required ? You can refer to : MicrobiomeAnalyst
And you can also read in the tree file to double check if the tree tips are actually matched.
The tree file is a Newick (.nwk) file and it will not upload to this thread as I received the error code ‘jpg, jpeg, png, gif, heic, heif, webp, pdf, csv, txt are the only file formats accepted’.
This tree file will run beta diversity when paired with the ASV ID table and the metadata, but I will only get ASV IDs instead of taxonomic names (ie. b9d21f760014f9b9f7ccade30933dad1 instead of Akkermansia) when running other analyses as the taxonomic names have not been given. When I generated the taxonomy table, Microbiomeanalyst processed the other metrics but I got the tree tips error code for beta diversity. I have the code below to generate the tree, but please let me know if something else needs to be used.
source activate qiime2-2022.2
qiime fragment-insertion sepp
–i-representative-sequences ./dada2_rep_seqs_FECAL_single.qza
–i-reference-database sepp-refs-silva-128.qza
–o-tree ./silva_tree_FECAL.qza
–o-placements ./silva_tree_placements_FECAL.qza
unzip silva_tree_FECAL.qza
Hello , I have received your tree file from your email. I saw that the tree labels are not connected with ASV table and taxonomy table as shown below:
These IDs should be same to link the information of the tree to your abundance data. I don’t quite get the problem you mentioned in the second post. If the labels are correct, it should work. You can describe it in more detail with figures if necessary.
A taxonomy table is required for MicrobiomeAnalyst either embed in the abundance table or as a separate table. Make sure the ASV ID labels are the same in abundance table, taxonomy table and the tree tips.
Please let me know if you have more questions.