Since my initial genome fasta was not accepted, I opted to use the downloaded version. The script tries to set an absolute path early on, using output_file=`realpath ${1}; but I'm currently working on a server where this tool is not installed. The script then continues, but only downloads the .gz files. From the looks of the second for loop, it should actually unzip the files and concatenate output to the specified output file and then run samtools.
Since my initial genome fasta was not accepted, I opted to use the downloaded version. The script tries to set an absolute path early on, using
output_file=`realpath ${1}; but I'm currently working on a server where this tool is not installed. The script then continues, but only downloads the .gz files. From the looks of the secondforloop, it should actually unzip the files and concatenate output to the specified output file and then run samtools.