Issue with getting reference genomes

Microbial community profiling PhyloPhlAn
1

Hello,

I have 17 MAGs/bins and I have annotated them so they belong to different classes. I want to pull genomes from the Genbank that are closely related to my MAGs. Here is my command for Actinomycetia class:

phylophlan_get_reference -g c__Actinomycetia -o genomes

But I get the following error:

[e] no reference genomes found for “c__Actinomycetia”, please check the taxonomic label provided

However, if I manually search in Genbank I do find many Actinomycetia genomes.

Could you please help me how can I pull genomes for a specific class, family or genus for the purpose of drawing phylogenitc tree to see how similar/dissimilar my MAGs are from the genomes already present in the Genbank?

Many thanks,

3

Hi and thanks for reporting this.
So, basically, the problem is with the label. The mapping of the taxonomy in PhyloPhlAn is from a couple of years ago and the class name “Actinomycetia” was after that. I think you will find all genomes you need by changing the taxonomic label to the old “c__Actinobacteria”.

Many thanks,
Francesco

4

Ok that one works.

Actually, I am having issue with pulling the genomes for newly renamed genomes for example, c__Andersenbacteria and p__Patescibacteria etc.

5

Also those labels changed quite recently and in the past were a bit messy.
I did this:

$ bzgrep -i patesci taxa2genomes_cpa201901_up201901.txt.bz2

2052139 k__Bacteria|p__Bacteria_unclassified|c__Bacteria_unclassified|o__Bacteria_unclassified|f__Bacteria_unclassified|g__Bacteria_unclassified|s__Patescibacteria_group_bacterium GCA_003142075.1;[..];GCA_008012035.1

and then

$ bzgrep -i anderse taxa2genomes_cpa201901_up201901.txt.bz2

1797278 k__Bacteria|p__Candidatus_Andersenbacteria|c__Candidatus_Andersenbacteria_unclassified|o__Candidatus_Andersenbacteria_unclassified|f__Candidatus_Andersenbacteria_unclassified|g__Candidatus_Andersenbacteria_unclassified|s__Candidatus_Andersenbacteria_bacterium_RIFCSPHIGHO2_01_FULL_46_36 GCA_001817035.1

The taxa2genomes_cpa201901_up201901.txt.bz2 is what PhyloPhlAn uses to download genomes. In your specific case, you might want to try specifying a different label with the -g param. In particular, for the two labels you are not finding, you can now try with s__Patescibacteria_group_bacterium and then with p__Candidatus_Andersenbacteria.

6

Thank you, that was helpful.