def launch_raxml(alignment,
model,
output_dir,
seed,
starting_trees=1,
parsimony=False,
bs_trees=0,
cores=16,
debug=False,
parse=False):
util.expect_file_exists(alignment)
util.make_path(output_dir)
prefix = os.path.join(output_dir, "raxml")
prefix += "_" + model.replace("+", "")
cmd = []
cmd.append("mpiexec")
cmd.append("-np")
cmd.append(str(cores))
cmd.append(common.raxml)
cmd.append("--msa")
cmd.append(alignment)
cmd.append("--model")
cmd.append(model)
cmd.append("--seed")
cmd.append(str(seed))
cmd.append("--blmin")
cmd.append(common.raxml_min_bl)
if (parse):
cmd.append("--parse")
cmd.append("--tree")
if (starting_trees > 0):
if (not parsimony):
cmd.append("rand{" + str(starting_trees) + "}")
prefix += "_rand" + str(starting_trees)
else:
cmd.append("pars{" + str(starting_trees) + "}")
prefix += "_pars" + str(starting_trees)
if (bs_trees > 0):
cmd.append("--boostrap")
cmd.append("--bs-trees")
cmd.append(str(bs_trees))
prefix += "_bs" + str(bs_trees)
prefix += "_seed" + str(seed)
cmd.append("--prefix")
cmd.append(prefix)
cmd.append('--force')
cmd.append('perf_threads')
launcher.submit(prefix, cmd, cores, debug)
def launch_modeltest(alignment, output_dir, seed, cores=16, debug=False):
try:
os.mkdir(output_dir)
except:
pass
cmd = []
prefix = os.path.join(output_dir, "modeltest")
prefix += "_seed" + str(seed)
cmd.append("mpiexec")
cmd.append("-np")
cmd.append(str(cores))
cmd.append(common.modeltest)
cmd.append("-i")
cmd.append(alignment)
cmd.append("-t")
cmd.append("mp")
cmd.append("-o")
cmd.append(prefix)
cmd.append("--force")
cmd.append("-h")
cmd.append("uigfr")
launcher.submit(prefix, cmd, cores, debug)
def launch_pargenes(alignment, model, output_dir, seed, rand_trees, pars_trees,
bs_trees, cores):
util.make_path_clean(output_dir)
debug = False
alignment_dir = os.path.join(output_dir, "alignments")
util.mkdirp(alignment_dir)
alignment_symlink = os.path.join(alignment_dir, common.pargenes_ali_name)
raxml_options_file = os.path.join(output_dir, "raxml_options.txt")
with open(raxml_options_file, "w") as writer:
writer.write("--model " + model + " ")
writer.write("--blmin " + common.raxml_min_bl + " ")
writer.write("--precision " + str(common.raxml_precision) + " ")
relative_symlink(alignment, alignment_symlink)
prefix = os.path.join(output_dir, "pargenes")
cmd = []
cmd.append("python")
cmd.append(common.pargenes)
cmd.append("-a")
cmd.append(alignment_dir)
cmd.append("-o")
cmd.append(os.path.join(output_dir, "pargenes_output"))
cmd.append("-r")
cmd.append(raxml_options_file)
cmd.append("--seed")
cmd.append(str(seed))
cmd.append("-s")
cmd.append(str(rand_trees))
cmd.append("-p")
cmd.append(str(pars_trees))
cmd.append("-b")
cmd.append(str(bs_trees))
cmd.append("-c")
cmd.append(str(cores))
cmd.append("--core-assignment")
cmd.append("low")
print(" ".join(cmd))
launcher.submit(prefix, cmd, cores, debug)