search

mariemorel / condor

ConDor: a workflow to detect convergent evolution in large protein alignments
7 stars 3 forks source link

ValueError: operands could not be broadcast together with shapes (20,20) (2,) #7

Closed MonsterLaplace closed 1 year ago

MonsterLaplace commented 1 year ago

When I run the test data, somthing wrong with this problem. Is there any solutions to solve this problems ? Thank you! pastml:ERROR:01:00:56 Frequencies given in parameters ([0.059954 0.055887]) do not sum up to one (0.115841),ignoring them. Traceback (most recent call last): File "/mnt/z/xb/miniconda3/envs/nextflow/bin/pastml", line 8, in sys.exit(main()) File "/mnt/z/xb/miniconda3/envs/nextflow/lib/python3.10/site-packages/pastml/acr.py", line 1107, in main pastml_pipeline(*vars(params)) File "/mnt/z/xb/miniconda3/envs/nextflow/lib/python3.10/site-packages/pastml/acr.py", line 532, in pastml_pipeline acr_results = acr(forest=roots, columns=columns, column2states=column2states, File "/mnt/z/xb/miniconda3/envs/nextflow/lib/python3.10/site-packages/pastml/acr.py", line 202, in acr model_instance = model2class[model](parameter_file=params, rate_matrix_file=rate_file, reoptimise=reoptimise, File "/mnt/z/xb/miniconda3/envs/nextflow/lib/python3.10/site-packages/pastml/models/CustomRatesModel.py", line 52, in init self.D_DIAGONAL, self.A, self.A_INV = get_diagonalisation(self.frequencies, self._rate_matrix) File "/mnt/z/xb/miniconda3/envs/nextflow/lib/python3.10/site-packages/pastml/models/generator.py", line 28, in get_diagonalisation Q = get_normalised_generator(frequencies, rate_matrix) File "/mnt/z/xb/miniconda3/envs/nextflow/lib/python3.10/site-packages/pastml/models/generator.py", line 47, in get_normalised_generator generator = rate_matrix frequencies ValueError: operands could not be broadcast together with shapes (20,20) (2,)

fredericlemoine commented 1 year ago

Hi, In order to reproduce the issue, can you give the exact command line you executed please? Thank you

MonsterLaplace commented 1 year ago

Hi, In order to reproduce the issue, can you give the exact command line you executed please? Thank you Thank you for your quick response. The command line i used is the same as which you displayed in the CONDOR program release page. When I downgrade the python version from 3.10 to 3.7.3, problem solved,. Test data was run successfuly. I guess the problem was the lateat version of numpy in python 3.10 . My own data is still running. If other problem happened, I will leave a message here in the near future.

fredericlemoine commented 1 year ago

Ok, thank you for the feedback. Do not hesitate if you have other problems.