def run_pargenes(args):
print_header(args)
start = time.time()
ret = 0
try:
ret = main_raxml_runner(args, arguments.parse_arguments(args))
except Exception as inst:
logger.info("[Error] " + str(type(inst)) + " " + str(inst))
sys.exit(1)
end = time.time()
logger.timed_log(start, "END OF THE RUN OF " + os.path.basename(__file__))
if (ret != 0):
logger.info("Something went wrong, please check the logs")
def run_pargenes(args):
start = time.time()
ret = 0
try:
op = arguments.parse_arguments(args)
except Exception as inst:
logger.info("[Error] " + str(type(inst)) + " " + str(inst))
sys.exit(1)
try:
ret = main_raxml_runner(args, op)
except Exception as inst:
logger.info("[Error] " + str(type(inst)) + " " + str(inst))
report.report_and_exit(op.output_dir, 1)
end = time.time()
logger.timed_log("END OF THE RUN OF " + os.path.basename(__file__))
if (ret != 0):
logger.info("Something went wrong, please check the logs")
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
p.wait()
if (0 != p.returncode):
logger.error("Astral execution failed")
report.report_and_exit(pargenes_dir, 1)
def run_astral_pargenes(astral_jar, op):
run_astral(op.output_dir, astral_jar, op.astral_global_parameters)
if (__name__ == '__main__'):
if (len(sys.argv) != 2 and len(sys.argv) != 3):
print("Error: syntax is:")
print("python astral.py pargenes_dir [astral_parameters_file]")
print(
"astral_parameters_file is optional and should contain additional parameters to pass to astral call)"
)
exit(1)
pargenes_dir = sys.argv[1]
parameters_file = None
if (len(sys.argv) > 2):
parameters_file = sys.argv[2]
start = time.time()
logger.init_logger(pargenes_dir)
logger.timed_log(start, "Starting astral pargenes script...")
scriptdir = os.path.dirname(os.path.realpath(__file__))
astral_jar = os.path.join(scriptdir, "..", "pargenes_binaries",
"astral.jar")
run_astral(pargenes_dir, astral_jar, parameters_file)
logger.timed_log(start, "End of astral pargenes script...")
