def bait(self, maskmiddle='f', k='19'):
        """
        Use bbduk to perform baiting
        :param maskmiddle: boolean argument treat the middle base of a kmer as a wildcard; increases sensitivity
        in the presence of errors.
        :param k: keyword argument for length of kmers to use in the analyses
        """
        logging.info('Performing kmer baiting of fastq files with {at} targets'.format(at=self.analysistype))
        # There seems to be some sort of issue with java incorrectly calculating the total system memory on certain
        # computers. For now, calculate the memory, and feed it into the bbduk call
        if self.kmer_size is None:
            kmer = k
        else:
            kmer = self.kmer_size
        with progressbar(self.runmetadata) as bar:
            for sample in bar:
                if sample.general.bestassemblyfile != 'NA' and sample[self.analysistype].runanalysis:
                    # Create the folder (if necessary)
                    make_path(sample[self.analysistype].outputdir)
                    # Make the system call
                    if len(sample.general.fastqfiles) == 2:
                        # Create the command to run the baiting - paired inputs and a single, zipped output
                        sample[self.analysistype].bbdukcmd = \
                            'bbduk.sh -Xmx{mem} ref={ref} in1={in1} in2={in2} k={kmer} maskmiddle={mm} ' \
                            'threads={c} outm={om}' \
                            .format(mem=self.mem,
                                    ref=sample[self.analysistype].baitfile,
                                    in1=sample.general.trimmedcorrectedfastqfiles[0],
                                    in2=sample.general.trimmedcorrectedfastqfiles[1],
                                    kmer=kmer,
                                    mm=maskmiddle,
                                    c=str(self.cpus),
                                    om=sample[self.analysistype].baitedfastq)
                    else:
                        sample[self.analysistype].bbdukcmd = \
                            'bbduk.sh -Xmx{mem} ref={ref} in={in1} k={kmer} maskmiddle={mm} ' \
                            'threads={cpus} outm={outm}' \
                            .format(mem=self.mem,
                                    ref=sample[self.analysistype].baitfile,
                                    in1=sample.general.trimmedcorrectedfastqfiles[0],
                                    kmer=kmer,
                                    mm=maskmiddle,
                                    cpus=str(self.cpus),
                                    outm=sample[self.analysistype].baitedfastq)
                    # Run the system call (if necessary)
                    if not os.path.isfile(sample[self.analysistype].baitedfastq):
                        out, err = run_subprocess(sample[self.analysistype].bbdukcmd)
                        write_to_logfile(sample[self.analysistype].bbdukcmd,
                                         sample[self.analysistype].bbdukcmd,
                                         self.logfile, sample.general.logout, sample.general.logerr,
                                         sample[self.analysistype].logout, sample[self.analysistype].logerr)
                        write_to_logfile(out,
                                         err,
                                         self.logfile, sample.general.logout, sample.general.logerr,
                                         sample[self.analysistype].logout, sample[self.analysistype].logerr)
Use bbduk to perform baiting
        :param maskmiddle: boolean argument treat the middle base of a kmer as a wildcard; increases sensitivity
        in the presence of errors.
        :param k: keyword argument for length of kmers to use in the analyses