test data?

[zhjilin]

Hi,
Thanks for developing this cool tool.
The description of HiC input files is a bit vague. Is it possible detailed documentation and a small test data somewhere to make sure the scripts are actually working properly?

Thanks!

[yangymargaret]

Hi zhjilin @zhjilin,
Thank you for your interest in Phylo-HMRF and thank you for this question. I'm sorry for the inadequate description of the Hi-C input files. I have added more description of the Hi-C input files in README, and uploaded a test dataset of four species to example_input/test_data/. Please see the README (updates are mainly in the description of path_list.txt) and the test data in the directory above. Please let me know if you have any other questions. Many thanks!

[zhjilin]

Hi @yangymargaret,
Thanks a lot for the swift reply and the test data. My apology for the late response. The input data kind of work except somehow we managed to get the following errors when running the same test data for several times. In addition, the program never exited naturally but halted right after the errors. The dependencies are exactly the same versions as the specified in the instructions. Any idea what caused this? It's appreciated if you could kindly help to identify, maybe give some suggestions to fix the problem.

Thanks!

phylo_hmrf.py:1061: RuntimeWarning: overflow encountered in exp
  beta1_exp = np.exp(-beta1)
phylo_hmrf.py:1072: RuntimeWarning: overflow encountered in double_scalars
  values[i,1] = ratio1[i]*(1-beta1_exp[i]**2) + values[p_idx[i],1]*(beta1_exp[i]**2)
phylo_hmrf.py:1072: 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)
phylo_hmrf.py:1071: RuntimeWarning: invalid value encountered in double_scalars
  values[i,0] = values[p_idx[i],0]*beta1_exp[i] + theta1[i]*(1-beta1_exp[i])
phylo_hmrf.py:1077: RuntimeWarning: overflow encountered in exp
  s2 = values[idx,1]*np.exp(-s1)

[yangymargaret]

Hi zhjilin @zhjilin,
Thank you for your question. Could you please try running the code with NumPy 1.13.3? I just found that the NumPy version I used to test the code is 1.13.3. I'm sorry for the inaccuracy on the dependencies described. But I'm not sure whether this is related to the errors you saw. Please see if this helps. Please let me know if you have any other questions. Thanks!

[zhjilin]

Hi @yangymargaret,
Many thanks for the quick reply. Seems like it finally ran through. I noticed there are some msgs as shown below. Should I ignore them?

state_id: 12
out of bound error! 1
state_id: 13
state_id: 14
state_id: 15
matrix not invertible! 10
OS error: SVD did not converge
matrix not invertible! 10
matrix not invertible! 10

Thanks!

[yangymargaret]

Hi zhjilin @zhjilin ,
Thank you for the question. You could ignore the messages. The program will try other initialization if it has the errors shown in the messages. Please let me know if you have any other questions. Thanks!