GTDB Forum

ID association in tree output

Hi all, I just started using GTDB and I am really impressed by this endeavor, wonderful work, and I’m excited to improve my working taxonomies!

I just ran the tool for the first time on some refseq complete genomes that I’m interested in, and it looks like the output tree has only the GTDB unique IDs or sometimes just the taxonomic rank plus taxa name (e.g. “g Leptolinea”). I’m wondering how I can associate these back to the original input IDs? I don’t see the GTDB ID column in the summary table either. Am I missing something?
Thanks a lot for clarification and continued work on this project. It’s a game changer.
-stephanie

Hi Stephanie,

If your input genomes has the name “MyGenome.fna” it will be called “MyGenome” in GTDB-Tk output tables and trees. This might be an issue with the program you are using to visualize the tree. I can recommend Dendroscope as being compatible with GTDB-Tk produced Newick files.

Cheers,
Donovan

Dear Donovan,
Thanks for your answer. I have looked at the tree file using a text editor and see the same issue that the nodes are named with only the GTDB IDs. This is the bac120.classify.tree file generated from the classify_wf command (no other tree files arrive in the final outputs so I presume this is the one expected). I’m working with iTol as my viewer, but I’ve also used figtree to double check, so I don’t think it’s an issue with the program. If the tree had given the input name I had for the genomes, there would be no issue. What I mean is that the tree gives an entirely new name (the gtdb unique id from the database) that I cannot associate back to my original IDs. Is this unexpected?
Thanks,
Stephanie

Hi Stephanie,

I’m not entirely following the issue here. GTDB-Tk does not change the names of input genomes or attempt to map them to the GTDB. All your query genomes passing QC should end up in the output with a name derived from the input filename (or the explicit name you gave them if using a batchfile). Perhaps you can send me an image and small dataset that illustrates the issue.

Cheers,
Donovan