def run_parsing_step(msas, library, scheduler_mode, parse_run_output_dir, cores, op):
""" Run raxml-ng --parse on each MSA to check it is valid and
to get its MSA dimensiosn """
parse_commands_file = os.path.join(parse_run_output_dir, "parse_command.txt")
parse_run_results = os.path.join(parse_run_output_dir, "results")
commons.makedirs(parse_run_results)
fasta_chuncks = []
fasta_chuncks.append([])
with open(parse_commands_file, "w") as writer:
for name, msa in msas.items():
fasta_output_dir = os.path.join(parse_run_results, name)
commons.makedirs(fasta_output_dir)
if (op.use_modeltest):
if (not msa.has_model()):
# set a fake model to make raxml parsing happy
# if will be replaced after modeltest run
if (op.datatype == "aa"):
msa.set_model("WAG")
else:
msa.set_model("GTR")
writer.write("parse_" + name + " 1 1 ")
writer.write(" --parse ")
writer.write(" --log DEBUG ")
writer.write( " --msa " + msa.path + " " + msa.get_raxml_arguments_str())
writer.write(" --prefix " + os.path.join(fasta_output_dir, name))
writer.write(" --threads 1 ")
writer.write("\n")
scheduler.run_mpi_scheduler(library, scheduler_mode, parse_commands_file, parse_run_output_dir, cores, op)
def run(output_dir, library, scheduler_mode, run_path, cores, op):
""" Use the MPI scheduler to run raxml --support on all the MSAs.
This call builds the trees withs support values from bootstraps"""
ml_trees_dir = os.path.join(output_dir, "mlsearch_run", "results")
concatenated_dir = os.path.join(output_dir, "concatenated_bootstraps")
commands_file = os.path.join(run_path, "supports_commands.txt")
commons.makedirs(run_path)
support_results = os.path.join(run_path, "results")
commons.makedirs(support_results)
logger.info("Writing supports commands in " + commands_file)
with open(commands_file, "w") as writer:
for fasta in os.listdir(ml_trees_dir):
ml_tree = os.path.join(ml_trees_dir, fasta,
fasta + ".raxml.bestTree")
bs_trees = os.path.join(concatenated_dir, fasta + ".bs")
if (not os.path.exists(bs_trees)
or os.stat(bs_trees).st_size == 0):
continue
writer.write("support_" + fasta + " 1 1")
writer.write(" --support")
writer.write(" --tree " + ml_tree)
writer.write(" --bs-trees " + bs_trees)
writer.write(" --threads 1")
writer.write(" --prefix " +
os.path.join(support_results, fasta + ".support"))
writer.write("\n")
scheduler.run_mpi_scheduler(library, scheduler_mode, commands_file,
run_path, cores, op)
def run(msas, output_dir, library, run_path, op):
""" Use the MPI scheduler to run modeltest on all the MSAs"""
cores = op.cores
run_path = os.path.join(output_dir, "modeltest_run")
commands_file = os.path.join(run_path, "modeltest_command.txt")
modeltest_results = os.path.join(run_path, "results")
commons.makedirs(modeltest_results)
if (op.modeltest_cores < 4):
print(
"[Error] The number of cores per modeltest job should at least be 4"
)
sys.exit(1)
with open(commands_file, "w") as writer:
for name, msa in msas.items():
if (not msa.valid):
continue
modeltest_fasta_output_dir = os.path.join(modeltest_results, name)
commons.makedirs(modeltest_fasta_output_dir)
writer.write("modeltest_" + name + " ")
writer.write(
str(op.modeltest_cores) + " " +
str(msa.taxa * msa.per_taxon_clv_size))
writer.write(" -i ")
writer.write(msa.path)
writer.write(" -t mp ")
writer.write(" -o " + os.path.join(modeltest_results, name, name))
writer.write(" " + msa.modeltest_arguments + " ")
writer.write("\n")
scheduler.run_mpi_scheduler(library, op.scheduler, commands_file, run_path,
cores, op)
def concatenate_bootstraps(output_dir, cores):
""" Concurrently run concatenate_bootstrap_msa on all the MSA (on one single node)"""
concatenated_dir = os.path.join(output_dir, "concatenated_bootstraps")
commons.makedirs(concatenated_dir)
bootstraps_dir = os.path.join(output_dir, "mlsearch_run", "bootstraps")
with concurrent.futures.ThreadPoolExecutor(
max_workers=min(16, int(cores))) as e:
for msa_name in os.listdir(bootstraps_dir):
e.submit(concatenate_bootstrap_msa, bootstraps_dir,
concatenated_dir, msa_name)
def concatenate_bootstraps(output_dir, cores):
""" Concurrently run concatenate_bootstrap_msa on all the MSA (on one single node)"""
concatenated_dir = os.path.join(output_dir, "concatenated_bootstraps")
commons.makedirs(concatenated_dir)
bootstraps_dir = os.path.join(output_dir, "mlsearch_run", "bootstraps")
pool = multiprocessing.Pool(processes=min(multiprocessing.cpu_count(), int(cores)))
for msa_name in os.listdir(bootstraps_dir):
pool.apply_async(concatenate_bootstrap_msa, (bootstraps_dir, concatenated_dir, msa_name,))
pool.close()
pool.join()
def run(msas, random_trees, parsimony_trees, bootstraps, library, scheduler_mode, run_path, cores, op):
""" Use the MPI scheduler_mode to run raxml-ng on all the dataset.
Also schedules the bootstraps runs"""
commands_file = os.path.join(run_path, "mlsearch_command.txt")
mlsearch_run_results = os.path.join(run_path, "results")
mlsearch_run_bootstraps = os.path.join(run_path, "bootstraps")
commons.makedirs(mlsearch_run_results)
starting_trees = random_trees + parsimony_trees
if (bootstraps != 0):
commons.makedirs(mlsearch_run_bootstraps)
with open(commands_file, "w") as writer:
for name, msa in msas.items():
if (not msa.valid):
continue
msa_path = msa.binary_path
if (msa_path == "" or msa_path == None):
msa_path = msa.path
msa_size = 1
if (not msa.flag_disable_sorting):
msa_size = msa.taxa * msa.per_taxon_clv_size
mlsearch_fasta_output_dir = os.path.join(mlsearch_run_results, name)
commons.makedirs(mlsearch_fasta_output_dir)
for starting_tree in range(0, starting_trees):
if (starting_trees > 1):
prefix = os.path.join(mlsearch_fasta_output_dir, "multiple_runs", str(starting_tree))
commons.makedirs(prefix)
prefix = os.path.join(prefix, name)
else:
prefix = os.path.join(mlsearch_fasta_output_dir, name)
writer.write("mlsearch_" + name + "_" + str(starting_tree) + " ")
writer.write(str(msa.cores) + " " + str(msa_size))
writer.write(" --msa " + msa_path + " " + msa.get_raxml_arguments_str())
writer.write(" --prefix " + prefix)
writer.write(" --threads 1 ")
if (starting_tree >= random_trees):
writer.write(" --tree pars ")
writer.write(" --seed " + str(starting_tree + op.seed + 1) + " ")
writer.write("\n")
bs_output_dir = os.path.join(mlsearch_run_bootstraps, name)
commons.makedirs(bs_output_dir)
chunk_size = 10
for current_bs in range(0, (bootstraps - 1) // chunk_size + 1):
bsbase = name + "_bs" + str(current_bs)
bs_number = min(chunk_size, bootstraps - current_bs * chunk_size)
writer.write(bsbase + " ")
writer.write(str(max(1, msa.cores // 2)) + " " + str(msa_size * chunk_size))
writer.write(" --bootstrap")
writer.write(" --msa " + msa_path + " " + msa.get_raxml_arguments_str())
writer.write(" --prefix " + os.path.join(bs_output_dir, bsbase))
writer.write(" --threads 1 ")
writer.write(" --seed " + str(current_bs + op.seed + 1))
writer.write(" --bs-trees " + str(bs_number))
writer.write("\n")
scheduler.run_mpi_scheduler(library, scheduler_mode, commands_file, run_path, cores, op)
def compute_constrain(msas, samples, raxml_library, scheduler_mode, run_path,
cores, op):
parsi_run_path = os.path.join(run_path, "parsimony")
parsi_commands_file = os.path.join(parsi_run_path, "command.txt")
parsi_results = os.path.join(parsi_run_path, "results")
commons.makedirs(parsi_results)
with open(parsi_commands_file, "w") as writer:
for name, msa in msas.items():
prefix = os.path.join(parsi_results, name)
if (not msa.valid):
continue
msa_path = msa.binary_path
if (msa_path == "" or msa_path == None):
msa_path = msa.path
msa_size = 1
writer.write("parsi_" + name + " 1 1")
writer.write(" --msa " + msa_path + " ")
writer.write(" --prefix " + os.path.abspath(prefix))
if (scheduler_mode != "fork"):
writer.write(" --threads 1 ")
writer.write(" --tree pars{" + str(samples) + "} ")
writer.write(" --start")
writer.write(" --model " + msa.get_model())
writer.write("\n")
scheduler.run_scheduler(raxml_library, scheduler_mode, "--threads",
parsi_commands_file, parsi_run_path, cores, op)
consensus_run_path = os.path.join(run_path, "consensus")
consensus_commands_file = os.path.join(consensus_run_path, "command.txt")
consensus_results = os.path.join(consensus_run_path, "results")
commons.makedirs(consensus_results)
with open(consensus_commands_file, "w") as writer:
for name, msa in msas.items():
prefix = os.path.join(consensus_results, name)
if (not msa.valid):
continue
trees = os.path.join(parsi_results, name + ".raxml.startTree")
writer.write("consensus_" + name + " 1 1")
writer.write(" --prefix " + os.path.abspath(prefix))
if (scheduler_mode != "fork"):
writer.write(" --threads 1 ")
writer.write(" --tree " + trees)
writer.write(" --consense STRICT")
writer.write("\n")
scheduler.run_scheduler(raxml_library, scheduler_mode, "--threads",
consensus_commands_file, consensus_run_path, cores,
op)
def run_parsing_step(msas, library, scheduler_mode, parse_run_output_dir,
cores, op):
""" Run raxml-ng --parse on each MSA to check it is valid and
to get its MSA dimensiosn """
parse_commands_file = os.path.join(parse_run_output_dir,
"parse_command.txt")
parse_run_results = os.path.join(parse_run_output_dir, "results")
commons.makedirs(parse_run_results)
fasta_chuncks = []
fasta_chuncks.append([])
with open(parse_commands_file, "w") as writer:
for name, msa in msas.items():
fasta_output_dir = os.path.join(parse_run_results, name)
commons.makedirs(fasta_output_dir)
writer.write("parse_" + name + " 1 1 ")
writer.write(" --parse ")
writer.write(" --log DEBUG ")
writer.write(" --msa " + msa.path + " " + msa.raxml_arguments)
writer.write(" --prefix " + os.path.join(fasta_output_dir, name))
writer.write(" --threads 1 ")
writer.write("\n")
scheduler.run_mpi_scheduler(library, scheduler_mode, parse_commands_file,
parse_run_output_dir, cores, op)
def main_raxml_runner(args, op):
""" Run pargenes from the parsed arguments op """
start = time.time()
output_dir = op.output_dir
checkpoint_index = checkpoint.read_checkpoint(output_dir)
if (os.path.exists(output_dir) and not op.do_continue):
logger.info(
"[Error] The output directory " + output_dir +
" already exists. Please use another output directory or run with --continue."
)
sys.exit(1)
commons.makedirs(output_dir)
logger.init_logger(op.output_dir)
print_header(args)
msas = None
logger.timed_log("end of MSAs initializations")
scriptdir = os.path.dirname(os.path.realpath(__file__))
modeltest_run_path = os.path.join(output_dir, "modeltest_run")
raxml_run_path = os.path.join(output_dir, "mlsearch_run")
binaries_dir = os.path.join(scriptdir, "..", "pargenes_binaries")
print("Binaries directory: " + binaries_dir)
if (op.scheduler != "split"):
raxml_library = os.path.join(binaries_dir, "raxml-ng")
modeltest_library = os.path.join(binaries_dir, "modeltest-ng")
else:
raxml_library = os.path.join(binaries_dir, "raxml-ng-mpi.so")
modeltest_library = os.path.join(binaries_dir, "modeltest-ng-mpi.so")
astral_jar = os.path.join(binaries_dir, "astral.jar")
if (len(op.raxml_binary) > 1):
raxml_library = op.raxml_binary
if (len(op.modeltest_binary) > 1):
modeltest_library = op.modeltest_binary
if (len(op.astral_jar) > 1):
astral_jar = op.astral_jar
astral_jar = os.path.abspath(astral_jar)
if (checkpoint_index < 1):
msas = commons.init_msas(op)
raxml.run_parsing_step(msas, raxml_library, op.scheduler,
os.path.join(output_dir, "parse_run"), op.cores,
op)
raxml.analyse_parsed_msas(msas, op)
checkpoint.write_checkpoint(output_dir, 1)
logger.timed_log("end of parsing mpi-scheduler run")
else:
msas = raxml.load_msas(op)
if (op.dry_run):
logger.info("End of the dry run. Exiting")
return 0
logger.timed_log("end of anlysing parsing results")
if (op.use_modeltest):
if (checkpoint_index < 2):
modeltest.run(msas, output_dir, modeltest_library,
modeltest_run_path, op)
logger.timed_log("end of modeltest mpi-scheduler run")
modeltest.parse_modeltest_results(op.modeltest_criteria, msas,
output_dir)
logger.timed_log("end of parsing modeltest results")
# then recompute the binary MSA files to put the correct model, and reevaluate the MSA sizes with the new models
shutil.move(os.path.join(output_dir, "parse_run"),
os.path.join(output_dir, "old_parse_run"))
raxml.run_parsing_step(msas, raxml_library, op.scheduler,
os.path.join(output_dir, "parse_run"),
op.cores, op)
raxml.analyse_parsed_msas(msas, op)
logger.timed_log("end of the second parsing step")
checkpoint.write_checkpoint(output_dir, 2)
if (checkpoint_index < 3):
raxml.run(msas, op.random_starting_trees, op.parsimony_starting_trees,
op.bootstraps, raxml_library, op.scheduler, raxml_run_path,
op.cores, op)
logger.timed_log("end of mlsearch mpi-scheduler run")
checkpoint.write_checkpoint(output_dir, 3)
if (op.random_starting_trees + op.parsimony_starting_trees > 1):
if (checkpoint_index < 4):
raxml.select_best_ml_tree(msas, op)
logger.timed_log("end of selecting the best ML tree")
checkpoint.write_checkpoint(output_dir, 4)
if (op.bootstraps != 0):
if (checkpoint_index < 5):
bootstraps.concatenate_bootstraps(output_dir, min(16, op.cores))
logger.timed_log("end of bootstraps concatenation")
checkpoint.write_checkpoint(output_dir, 5)
starting_trees = op.random_starting_trees + op.parsimony_starting_trees
if (checkpoint_index < 6 and starting_trees > 0):
bootstraps.run(msas, output_dir, raxml_library, op.scheduler,
os.path.join(output_dir, "supports_run"), op.cores,
op)
logger.timed_log("end of supports mpi-scheduler run")
checkpoint.write_checkpoint(output_dir, 6)
if (op.use_astral):
if (checkpoint_index < 7):
astral.run_astral_pargenes(astral_jar, op)
checkpoint.write_checkpoint(output_dir, 7)
all_invalid = True
for name, msa in msas.items():
if (msa.valid):
all_invalid = False
if (all_invalid):
print("[Error] ParGenes failed to analyze all MSAs.")
report.report_and_exit(op.output_dir, 1)
print_stats(op)
return 0
def main_raxml_runner(op):
""" Run pargenes from the parsed arguments op """
start = time.time()
output_dir = op.output_dir
checkpoint_index = checkpoint.read_checkpoint(output_dir)
print("Checkpoint: " + str(checkpoint_index))
if (os.path.exists(output_dir) and not op.do_continue):
print(
"[Error] The output directory " + output_dir +
" already exists. Please use another output directory or run with --continue."
)
sys.exit(1)
commons.makedirs(output_dir)
logs = commons.get_log_file(output_dir, "pargenes_logs")
print("Redirecting logs to " + logs)
sys.stdout = open(logs, "w")
print_header()
msas = commons.init_msas(op)
timed_print(start, "end of MSAs initializations")
scriptdir = os.path.dirname(os.path.realpath(__file__))
modeltest_run_path = os.path.join(output_dir, "modeltest_run")
raxml_run_path = os.path.join(output_dir, "mlsearch_run")
if (op.scheduler == "onecore"):
raxml_library = os.path.join(scriptdir, "..", "raxml-ng", "bin",
"raxml-ng")
modeltest_library = os.path.join(scriptdir, "..", "modeltest", "bin",
"modeltest-ng")
else:
raxml_library = os.path.join(scriptdir, "..", "raxml-ng", "bin",
"raxml-ng-mpi.so")
modeltest_library = os.path.join(scriptdir, "..", "modeltest", "build",
"src", "modeltest-ng-mpi.so")
if (checkpoint_index < 1):
raxml.run_parsing_step(msas, raxml_library, op.scheduler,
os.path.join(output_dir, "parse_run"), op.cores,
op)
checkpoint.write_checkpoint(output_dir, 1)
timed_print(start, "end of parsing mpi-scheduler run")
raxml.analyse_parsed_msas(msas, op, output_dir)
if (op.dry_run):
print("End of the dry run. Exiting")
return 0
timed_print(start, "end of anlysing parsing results")
if (op.use_modeltest):
if (checkpoint_index < 2):
modeltest.run(msas, output_dir, modeltest_library,
modeltest_run_path, op)
timed_print(start, "end of modeltest mpi-scheduler run")
modeltest.parse_modeltest_results(op.modeltest_criteria, msas,
output_dir)
timed_print(start, "end of parsing modeltest results")
# then recompute the binary MSA files to put the correct model, and reevaluate the MSA sizes with the new models
shutil.move(os.path.join(output_dir, "parse_run"),
os.path.join(output_dir, "old_parse_run"))
raxml.run_parsing_step(msas, raxml_library, op.scheduler,
os.path.join(output_dir, "parse_run"),
op.cores, op)
raxml.analyse_parsed_msas(msas, op, output_dir)
timed_print(start, "end of the second parsing step")
checkpoint.write_checkpoint(output_dir, 2)
if (checkpoint_index < 3):
raxml.run(msas, op.random_starting_trees, op.parsimony_starting_trees,
op.bootstraps, raxml_library, op.scheduler, raxml_run_path,
op.cores, op)
timed_print(start, "end of mlsearch mpi-scheduler run")
checkpoint.write_checkpoint(output_dir, 3)
if (op.random_starting_trees + op.parsimony_starting_trees > 1):
if (checkpoint_index < 4):
raxml.select_best_ml_tree(msas, op)
timed_print(start, "end of selecting the best ML tree")
checkpoint.write_checkpoint(output_dir, 4)
if (op.bootstraps != 0):
if (checkpoint_index < 5):
bootstraps.concatenate_bootstraps(output_dir, min(16, op.cores))
timed_print(start, "end of bootstraps concatenation")
checkpoint.write_checkpoint(output_dir, 5)
if (checkpoint_index < 6):
bootstraps.run(output_dir, raxml_library, op.scheduler,
os.path.join(output_dir, "supports_run"), op.cores,
op)
timed_print(start, "end of supports mpi-scheduler run")
checkpoint.write_checkpoint(output_dir, 6)
return 0
