I would like to download all genomes of the specific species, which representative 's CheckM Completeness = 100. So i used advanced search like this. But i only got the GTDB Representative of Species. Other genomes in the species is missing. How can i download them in batches
You are only getting the GTDB representative genomes as you have set “GTDB Representative of Species” to TRUE. If you remove this filter, you should get all genomes. The “Genomes” button with the down arrow will produce a script you can run on your local computer to download the genomes from NCBI.