def annotatethreads(self):
        """
        Use prokka to annotate each strain
        """
        # Move the files to subfolders and create objects
        self.runmetadata = createobject.ObjectCreation(self)
        # Fix headers
        self.headers()
        printtime('Performing prokka analyses', self.start)
        # Create and start threads
        for i in range(self.cpus):
            # Send the threads to the appropriate destination function
            threads = Thread(target=self.annotate, args=())
            # Set the daemon to true - something to do with thread management
            threads.setDaemon(True)
            # Start the threading
            threads.start()
        for sample in self.metadata.samples:
            # Create the prokka attribute in the metadata object
            setattr(sample, 'prokka', GenObject())
            sample.prokka.outputdir = os.path.join(sample.general.outputdirectory, 'prokka')
            if not os.path.isdir(sample.prokka.outputdir):
                os.makedirs(sample.prokka.outputdir)
            # TODO Incorporate MASH/rMLST/user inputted genus, species results in the system call
            # Create the system call
            # prokka 2014-SEQ-0275.fasta --force --genus Escherichia --species coli --usegenus --addgenes
            # --prefix 2014-SEQ-0275 --locustag EC0275 --outputdir /path/to/sequences/2014-SEQ-0275/prokka
            sample.prokka.command = 'prokka {} ' \
                                    '--force ' \
                                    '--genus {} ' \
                                    '--species {} ' \
                                    '--usegenus ' \
                                    '--addgenes ' \
                                    '--prefix {} ' \
                                    '--locustag {} ' \
                                    '--outdir {}' \
                .format(sample.general.fixedheaders,
                        self.genus, self.species, sample.name, sample.name, sample.prokka.outputdir)
            self.queue.put(sample)
        self.queue.join()
Use prokka to annotate each strain