Error using example input

[cyz0315]

I tried to run with example input with command
python phylo_hmrf.py -n 20 -p $input_dir -r 1 --reload 0 --chromvec 21,22 --miter 100.
$input_dir to Phylo-HMRF-master/example_input.

But I got this error.

out of bound error! 1
out of bound error! 2
out of bound error! 3
ou_optimize_init likelihood -10.2005793894
number in the cluster 12511 8
out of bound error! 1
/home/cheyizhuo/project/cross_Fo_HiC/mycode/Phylo-HMRF-master/phylo_hmrf.py:1257: RuntimeWarning: divide by zero encountered in divide
ratio1 = lambda1/(2beta1)
/home/cheyizhuo/project/cross_Fo_HiC/mycode/Phylo-HMRF-master/phylo_hmrf.py:1271: RuntimeWarning: invalid value encountered in double_scalars
values[i,1] = ratio1[i](1-beta1_exp[i]**2) + values[p_idx[i],1]*(beta1_exp[i]**2)
Traceback (most recent call last):
File "/home/cheyizhuo/project/cross_Fo_HiC/mycode/Phylo-HMRF-master/phylo_hmrf.py", line 1760, in
opts.simu_version, opts.annotation, opts.reload, opts.dtype, opts.miter, opts.resolution, opts.quantile, opts.ref_species, opts.output)
File "/home/cheyizhuo/project/cross_Fo_HiC/mycode/Phylo-HMRF-master/phylo_hmrf.py", line 1738, in run
params_vec1, params_vec2, params_vecList, iter_id1, iter_id2, cost_vec, state_vec = tree1.fit_accumulate_test(samples, len_vec, threshold, filename, m_iter)
File "/home/cheyizhuo/project/cross_Fo_HiC/mycode/Phylo-HMRF-master/base.py", line 307, in fit_accumulate_test
self._init(X, lengths=lengths)
File "/home/cheyizhuo/project/cross_Fo_HiC/mycode/Phylo-HMRF-master/phylo_hmrf.py", line 246, in _init
self.init_ou_params = self.init_ou_param(X1[0:select_num1], init_label[0:select_num1], self.means)
File "/home/cheyizhuo/project/cross_Fo_HiC/mycode/Phylo-HMRF-master/phylo_hmrf.py", line 196, in _init_ou_param
cur_param, lik = self._ou_optimize_init(x1, mean_values[i])
File "/home/cheyizhuo/project/cross_Fo_HiC/mycode/Phylo-HMRF-master/phylo_hmrf.py", line 1438, in _ou_optimize_init
flag, params1 = self._ou_optimize_init_unit(X, mean_values)
File "/home/cheyizhuo/project/cross_Fo_HiC/mycode/Phylo-HMRF-master/phylo_hmrf.py", line 1493, in _ou_optimize_init_unit
constraints=con1, tol=1e-6, options={'disp': False})
File "/home/cheyizhuo/miniconda3/envs/py27/lib/python2.7/site-packages/scipy/optimize/_minimize.py", line 458, in minimize
constraints, callback=callback, **options)
File "/home/cheyizhuo/miniconda3/envs/py27/lib/python2.7/site-packages/scipy/optimize/slsqp.py", line 370, in _minimize_slsqp
raise ValueError("Objective function must return a scalar")
ValueError: Objective function must return a scalar

[cyz0315]

This problem occurred randomly. It appears when using function _init (line 204 in phylo_hmrf.py), wrong initiation could be generated. If you run this script multiple times, it may succeed.

[yangymargaret]

Hi @cyz0315,
Thank you very much for helping identify this problem. I am very sorry for my late reply. I think the problem occurs due to cases of random initiation where the program did not find a solution. The program includes some mechanism of restarting initialization if a solution cannot be found, but it is incomplete. I will update the part of restarting initialization accordingly. Please let me know if you have any other questions. Many thanks!

Best regards!
Yang Yang