An application for parameterization of biological models available in SBML and BNGL formats. Features include parallelization, metaheuristic optimization algorithms, and an adaptive Markov chain Monte Carlo (MCMC) sampling algorithm.
I get the following error when using Metropolis-Hastings:
/home/---/anaconda3/envs/refmodel/lib/python3.10/site-packages/pybnf/algorithms.py:1991: UserWarning: genfromtxt: Empty input file: "/home/---/PycharmProjects/EGFR_reference_models/src//Results/samples.txt"
dat_array = np.genfromtxt(self.samples_file, delimiter='\t', dtype=float,
Sorry, an unknown error occurred: IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
2023-07-14 21:25:59,712 pybnf.pybnf ERROR MainProcess Internal error
Traceback (most recent call last):
File "/home/---/anaconda3/envs/refmodel/lib/python3.10/site-packages/pybnf/pybnf.py", line 229, in main
alg.run(cluster.client, resume=pending, debug=debug)
File "/home/---/anaconda3/envs/refmodel/lib/python3.10/site-packages/pybnf/algorithms.py", line 927, in run
response = self.got_result(res)
File "/home/---/anaconda3/envs/refmodel/lib/python3.10/site-packages/pybnf/algorithms.py", line 2306, in got_result
self.update_histograms('_final')
File "/home/---/anaconda3/envs/refmodel/lib/python3.10/site-packages/pybnf/algorithms.py", line 2006, in update_histograms
histdata = np.log10(dat_array[:, i])
IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
2023-07-14 21:25:59,713 pybnf.cluster INFO MainProcess Closing client
2023-07-14 21:26:00,056 pybnf.pybnf INFO MainProcess Fitting unsuccessful. Attempting cleanup
2023-07-14 21:26:00,056 pybnf.algorithms INFO MainProcess Outputting results to file /home/---/PycharmProjects/EGFR_reference_models/src//Results/sorted_params_end.txt
2023-07-14 21:26:00,059 pybnf.pybnf ERROR MainProcess During cleanup, another exception occurred
Traceback (most recent call last):
File "/home/---/anaconda3/envs/refmodel/lib/python3.10/site-packages/pybnf/pybnf.py", line 394, in main
alg.cleanup()
File "/home/---/anaconda3/envs/refmodel/lib/python3.10/site-packages/pybnf/algorithms.py", line 2479, in cleanup
super().cleanup()
File "/home/---/anaconda3/envs/refmodel/lib/python3.10/site-packages/pybnf/algorithms.py", line 2030, in cleanup
self.update_histograms('_end')
File "/home/---/anaconda3/envs/refmodel/lib/python3.10/site-packages/pybnf/algorithms.py", line 2006, in update_histograms
histdata = np.log10(dat_array[:, i])
IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
2023-07-14 21:26:00,059 pybnf.pybnf INFO MainProcess Total fitting time: 0:00:12
It appears to run normally until it tries to construct the histogram at the end. Suggestions?
Hi,
I get the following error when using Metropolis-Hastings:
/home/---/anaconda3/envs/refmodel/lib/python3.10/site-packages/pybnf/algorithms.py:1991: UserWarning: genfromtxt: Empty input file: "/home/---/PycharmProjects/EGFR_reference_models/src//Results/samples.txt" dat_array = np.genfromtxt(self.samples_file, delimiter='\t', dtype=float, Sorry, an unknown error occurred: IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
The conf file is the following:
model = EGFR_module.xml : egfrpSD.exp
output_dir=/home/---/PycharmProjects/EGFR_reference_models/src/
fit_type = mh objfunc = chi_sq population_size=1 max_iterations=100
loguniform_var = k1 0.001 1 loguniform_var = k_1 0.001 1 loguniform_var = kt 0.001 1 loguniform_var = ke 0.001 1 loguniform_var = Vr 0.001 1 loguniform_var = kx 0.001 1 loguniform_var = kh 0.001 1 loguniform_var = k3 0.001 1 loguniform_var = k_3 0.001 1
verbosity=1
time_course = model:EGFR_module, time:100, suffix:egfrpSD
And here is the tail of the log file:
2023-07-14 21:25:59,712 pybnf.pybnf ERROR MainProcess Internal error Traceback (most recent call last): File "/home/---/anaconda3/envs/refmodel/lib/python3.10/site-packages/pybnf/pybnf.py", line 229, in main alg.run(cluster.client, resume=pending, debug=debug) File "/home/---/anaconda3/envs/refmodel/lib/python3.10/site-packages/pybnf/algorithms.py", line 927, in run response = self.got_result(res) File "/home/---/anaconda3/envs/refmodel/lib/python3.10/site-packages/pybnf/algorithms.py", line 2306, in got_result self.update_histograms('_final') File "/home/---/anaconda3/envs/refmodel/lib/python3.10/site-packages/pybnf/algorithms.py", line 2006, in update_histograms histdata = np.log10(dat_array[:, i]) IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed 2023-07-14 21:25:59,713 pybnf.cluster INFO MainProcess Closing client 2023-07-14 21:26:00,056 pybnf.pybnf INFO MainProcess Fitting unsuccessful. Attempting cleanup 2023-07-14 21:26:00,056 pybnf.algorithms INFO MainProcess Outputting results to file /home/---/PycharmProjects/EGFR_reference_models/src//Results/sorted_params_end.txt 2023-07-14 21:26:00,059 pybnf.pybnf ERROR MainProcess During cleanup, another exception occurred Traceback (most recent call last): File "/home/---/anaconda3/envs/refmodel/lib/python3.10/site-packages/pybnf/pybnf.py", line 394, in main alg.cleanup() File "/home/---/anaconda3/envs/refmodel/lib/python3.10/site-packages/pybnf/algorithms.py", line 2479, in cleanup super().cleanup() File "/home/---/anaconda3/envs/refmodel/lib/python3.10/site-packages/pybnf/algorithms.py", line 2030, in cleanup self.update_histograms('_end') File "/home/---/anaconda3/envs/refmodel/lib/python3.10/site-packages/pybnf/algorithms.py", line 2006, in update_histograms histdata = np.log10(dat_array[:, i]) IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed 2023-07-14 21:26:00,059 pybnf.pybnf INFO MainProcess Total fitting time: 0:00:12
It appears to run normally until it tries to construct the histogram at the end. Suggestions?