Output missing large sections of sequence. #20
Description
Input reference is a .gbff file from NCBI and the input sequences are 100 .fna files from NCBI. I do not experience any errors in running parsnp on the command line. Additionally, I checked to make sure that all of the strains were (reasonably) related and they all shared 97-100% identity. Further, I checked the annotated file for the regions missing and they are present in the .gbff file.