I have downloaded all the microbial genome ( 71,782 genome) using the repophlan_get_microbes.py. and further, I got the quality score for each of these genomes.

Finally, I got 54382 good quality genome. But now I am not sure how should I filter these genome based on the ID.

Genome ID text is like this;

G001281285
G000014725
G000775715
G000254175
G001380675
G900057405

and within the fna folder, each microbial genome file are like this:

fna/

G001284865.fna.bz2  G002910165.fna.bz2  G009390615.fna.bz2
G001284885.fna.bz2  G002910195.fna.bz2  G009390655.fna.bz2

Many thanks nabiyogesh