GTDB output advise - tree file

Bacterial Taxonomy
1

Hi,
This is the first time that I use GTDB and I would like to have some advise on the output files. I have one bacterial genome (8.6 Mb) from the genus Streptomyces, the instance where I ran de tool had 240 GB of RAM and 400 GB of memory. After running GTDB (gene calling, align and classify) I got two output files, (a) tree and (b) summary.

When I visualized the tree on iTOL I realized that none of the species were related to my genome but the summary file was correct. But maybe I got confused about the tree file, should this tree be related to my genome?

Thanks four your time
Juan

2

Hi,

I don’t believe iTOL properly renders the tree. I’d recommend visualizing the tree with Dendroscope. Your genome will be in the tree file. You can verify this by opening the tree in a text editor and searching for the name of your genome (i.e. name of the input FASTA file).

Cheers,
Donovan