run IQ-Tree

def run_iqtree(phy, model, threads, cluster, node):
    """
    run IQ-Tree
    """
    # set ppn based on threads
    if threads > 24:
        ppn = 24
    else:
        ppn = threads
    tree = '%s.treefile' % (phy)
    if check(tree) is False:
        if model is False:
            model = 'TEST'
        dir = os.getcwd()
        command = 'iqtree-omp -s %s -m %s -nt %s -quiet' % \
                    (phy, model, threads)
        if cluster is False:
            p = Popen(command, shell = True)
        else:
            if node is False:
               node = '1'
            qsub = 'qsub -l nodes=%s:ppn=%s -m e -N iqtree' % (node, ppn)
            command = 'cd /tmp; mkdir iqtree; cd iqtree; cp %s/%s .; %s; mv * %s/; rm -r ../iqtree' \
                    % (dir, phy, command, dir)
            re_call = 'cd %s; %s --no-fast --iq' % (dir.rsplit('/', 1)[0], ' '.join(sys.argv))
            p = Popen('echo "%s;%s" | %s' % (command, re_call, qsub), shell = True)
        p.communicate()
    return tree