I want to do pan genomics study of a bacterial group, it has got 147 strains with whole genome available at NCBI website. I downloaded the genebank, genebank (full) and fasta files for each strain. I am using BPGA version 1.3 for my study. The software works fine with Genebank (full) files but shows error for genebank files. I have genebank full files for only 95 strains as for other strains data is not available in NCBI database or it is deleted. I already used RASTA server for the file in which BGPA was showing error after annotation I downloaded the .gbk file and used in BGPA but it showed the same error. I wonder if there is any way to fix the broken gene bank files to be used in BGPA for pan genomics study. I want to find the same and different genes in all the strains and then design primers for them to be used in multiplex PCR. I wonder if i m on the correct path and which other tools will I need for my work and how to post process the results of BGPA and also what things should I consider or check out before staring pan genomics study ????

i am also attaching the image for the error i am facing