using?

[wwwt113]

I have a question about this: raceback (most recent call last): File "/home/Downloads/Promotech/promotech.py", line 79, in parseGenome40NTSequences( File "/home/Downloads/Promotech/genome/process_genome.py", line 81, in parseGenome40NTSequences chrom, cutted_seqs = genomeSlidingWindow(fasta_file_path=fasta_file_path, log_file=log_file, promoter_size=promoter_size, step_size=step_size, print_fn=print_fn) File "/home/Downloads/Promotech/genome/process_genome.py", line 52, in genomeSlidingWindow cutted_seqs = np.array([ genome[i:i+promoter_size] for i in progressbar.progressbar( range( 0, n_samples, step_size ) ) ]) TypeError: 'module' object is not callable and I don't know how to solve it, please help me. This is getting on my nerves.

[BioinformaticsLabAtMUN]

Are you using the conda environment we provided to run promotech?

[Bin-Ma]

Hi @BioinformaticsLabAtMUN , I have the same problem. I tried to employ the promotech in testing dataset with the command python promotech.py -pg -m RF-HOT -f examples/genome/ECOLI_2.fasta -o results. I confirm the promotech was employed in promotech_env.

Bin

[Bin-Ma]

Hi @wwwt113 , I solve the problem ! You can try to check the version of progressbar. I remove the progressbar package from pip and conda, and reinstall it by pip with the command pip install progressbar2. Finally, the promotech worked well.

Bin

[wwwt113]

Hi @wwwt113 , I solve the problem ! You can try to check the version of progressbar. I remove the progressbar package from pip and conda, and reinstall it by pip with the command pip install progressbar2. Finally, the promotech worked well.

Bin

Hi @Bin-Ma , Thank you for your answer. I did not use conda, so there was an error, but after changing the version of scipy, the promotech was ready to run. pip install scipy ==1.8.1 Like that. Thank you again for your peply.

_

[BioinformaticsLabAtMUN]

Thank you for indicating how you solved the issue!

As a reference the packages version we used are these: absl_py==0.15.0 astunparse==1.6.3 backcall==0.2.0 biopython==1.79 CacheControl==0.12.10 cachetools==4.2.4 certifi==2021.10.8 charset_normalizer==2.0.12 cycler==0.11.0 Cython==0.29.24 dataclasses==0.8 decorator==5.1.1 flatbuffers==1.12 gast==0.3.3 google-pasta==0.2.0 google_auth==2.3.3 google_auth_oauthlib==0.4.6 grpcio==1.32.0 h5py==2.10.0 hdmedians==0.14.1 idna==3.3 importlib_metadata==4.8.1 ipython==7.16.1 ipython_genutils==0.2.0 jedi==0.18.1 joblib==1.1.0 keras==2.8.0 Keras-Preprocessing==1.1.2 kiwisolver==1.3.1 lockfile==0.12.2 Markdown==3.3.6 matplotlib==3.3.4 msgpack==0.6.2 natsort==8.1.0 numpy==1.19.5 oauthlib==3.1.1 opt-einsum==3.3.0 pandas==1.0.3 parso==0.8.3 pexpect==4.8.0 pickleshare==0.7.5 Pillow==8.1.2 progressbar2==3.53.1 prompt_toolkit==3.0.29 protobuf==3.19.4 ptyprocess==0.7.0 pyasn1==0.4.8 pyasn1-modules==0.2.8 Pygments==2.11.2 pyparsing==3.0.8 PyQt5==5.15.1 PyQt5-sip==12.8.1 python-dateutil==2.8.2 python-utils==2.5.6 pytz==2022.1 requests==2.27.1 requests-oauthlib==1.3.0 rsa==4.8 scikit-bio==0.5.6 scikit-learn==0.23.2 scipy==1.4.1 six==1.15.0 tensorboard==2.8.0 tensorboard-data-server==0.6.1 tensorboard-plugin-wit==1.8.0 tensorflow==2.4.1 tensorflow-estimator==2.4.0 termcolor==1.1.0 threadpoolctl==3.1.0 traitlets==4.3.3 typing-extensions==3.7.4.3 urllib3==1.26.9 wcwidth==0.2.5 Werkzeug==2.0.3 wrapt==1.12.1 XlsxWriter==3.0.2 zipp==3.6.0