Create and run the plasmid extractor system call

def run_plasmid_extractor(self):
        """
        Create and run the plasmid extractor system call
        """
        logging.info('Extracting plasmids')
        # Define the system call
        extract_command = 'PlasmidExtractor.py -i {inf} -o {outf} -p {plasdb} -d {db} -t {cpus} -nc' \
            .format(inf=self.path,
                    outf=self.plasmid_output,
                    plasdb=os.path.join(self.plasmid_db, 'plasmid_db.fasta'),
                    db=self.plasmid_db,
                    cpus=self.cpus)
        # Only attempt to extract plasmids if the report doesn't already exist
        if not os.path.isfile(self.plasmid_report):
            # Run the system calls
            out, err = run_subprocess(extract_command)
            # Acquire thread lock, and write the logs to file
            self.threadlock.acquire()
            write_to_logfile(extract_command, extract_command, self.logfile)
            write_to_logfile(out, err, self.logfile)
            self.threadlock.release()