After performing a Roary analysis, some .gff files are missing during the visualization step using roary_plots

[jiangjiani0910-hue]

Hello all,
I first used PlasFlow to separate my FASTA files into plasmid and chromosome FASTA files, then annotated each with Prokka to obtain their respective GFF files. When I used Roary to analyze the plasmid and chromosome GFF files separately, I found that the resulting files (accessory_binary_genes.fa.newick and gene_presence_absence.csv) are missing a few genomes. What could be the reason for this?
Thanks!