Hi! I am writing to know if anyone else before has tried using the EMU tool with the GTDB database
(Files · master · treangenlab / Emu · GitLab).
I have been trying to create an EMU database without success, and I cannot figure out why. To create a database, EMU requires three files: a database file, a taxonomy file (containing the same headline as the database and the taxids), and finally either the nodes.dmp and names.dmp files, which I downloaded from here Releases · shenwei356/gtdb-taxdump · GitHub, or an additional file containing complete taxonomic lineages.
I have adapted the taxonomy file found on the GTDB database with the corresponding taxids by checking the metadata file, and I have tried using both the names.dmp/nodes.dmp file and the complete taxonomy file. In either case, I get some error, mainly about lack of correspondence between files.
Does someone have experience with both GTDB and EMU, or even just with the file format, and can understand what is going on? I am sorry but I am pretty new and I can’t figure out why I keep getting errors even when my files satisfy the requirements. Thank you in advance for any potential contribution!