The number of pan-genes in gene_presence_absence.csv is less than each genome

[Amilycd]

Hi, I encounterd a problem when using roary v3.13.0. I want to perform pan-analysis for Mycoplasma pneumoniae, the number of genes in each of the gff files is about 800, however, the total gene number in the summary file generated by roary is only 317. What happens? how can I solve it? In addtion, I also get an error of "Use of uninitialized value in require at /workdir/miniconda3/envs/roary/lib/site_perl/5.26.2/x86_64-linux-thread-multi/Encode.pm line 61."