I'm using refRANK to determine the most suitable reference genome to use for downstream analysis on some fastq STEC sequences. I downloaded around 70 STEC genomes from NCBI, transferred them to HPC and unzipped the tar file so they are now in genomic.fna format. However, each time I run the script its returning an error saying Assembly_genomic.fna contains multiple FASTA entries. Anyone have any ideas on how to solve this? Any advice would be much appreciated. The script is outlined below.
module load python3.7/i2
python refrank.py --fastq *.fastq.gz --ref *.fna