How to read three genome file formats together

[makerer5]

hi I want to use pgcgap to construct a whole genome phylogenetic tree of 120 strains. I used pgcgap to read in the genome file, but it seems that pgcgap can only read files of the same format. However, my 120 genomes contain three formats of files: double-end R1.fq.gz, R2.fq.gz; single-end .fq.gz (downloaded from NCBI); genbank (.gb). How can I read in 120 genome files in three formats using the following command: pgcgap --All --platform illumina --filter_length 200 --ReadsPath Reads/Illumina --reads1 _1.fastq.gz --reads2 _2.fastq.gz --suffix_len 11 --kmmer 81 --genus Escherichia --species coli --codon 11 --strain_num 6 --threads 4 --VAR --refgbk /mnt/h/PGCGAP_Examples/Reads/MG1655.gbff --qualtype sanger