I have two genomes namely ‘bin.SY63.6’ and ‘bin.SY19.18’ have confused results. Both of them were identified as “d__Bacteria;p__JADFOP01;c__JADFOP01;o__JADFOP01;f__JADFOP01;g__JADFOP01;s__JADFOP01 sp022562795” by the ANI step of the ‘classfy_wf’ command. However, when I run the ‘identify’ and ‘align’ commands to get the sequences of marker genes, these two genomes was identified as archaea and present in the archaeal MSA… It is very strange. The version of gtdb-tk that I used is v2.3.2. By the way, if I add option ‘–skip_ani_screen’ for the ‘classfy_wf’ command or just use the ‘de_novo_wf’ command, these two genomes was identified as archaea ‘d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__RBG-16-68-12;f__JAJISG01;g__;s__’.