IndexError

[MA-Kochen]

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?