AttributeError: 'NoneType' object has no attribute 'group'

[helan-1997]

Hi,

When I use DeepTE.py, I meet an error like this : ./DeepTE_domain.py -d ./working_dir -o ./output_dir -i result.fa -s ./supfile_dir --hmmscan hmmscan ./DeepTE.py -d ./working_dir -o ./output_dir -i result.fa -m_dir /home/user/biosoft/DeepTE/ -sp M -fam All -modify ./output_dir/opt_te_domain_pattern.txt then Using TensorFlow backend. start time is 1663231460.5417993 Step1: transfer fasta data to CNN input data Step2: classify TEs Step2: 1) domain information is exist Traceback (most recent call last): File "./DeepTE.py", line 274, in <module> main() File "./DeepTE.py", line 243, in main pipeline_yes_m.classify_pipeline(model_dir, input_CNN_data_file, temp_store_opt_dir, sp_type,te_domain_pattern_dic,te_fam,prop_thr) File "/home/user/biosoft/DeepTE/scripts/DeepTE_pipeline_yes_modification.py", line 508, in classify_pipeline model_nm = mt.group(1) AttributeError: 'NoneType' object has no attribute 'group'

[yanhaidong1]

Hey,

Would you try to run './DeepTE.py -d ./working_dir -o ./output_dir -i result.fa -m_dir /home/user/biosoft/DeepTE/ -sp M -modify ./output_dir/opt_te_domain_pattern.txt' without specifying '-fam All' using the current version of DeepTE? The current has updated to delete the '-fam All', and the default setting will directly classify all TEs.

Best wishes, Haidong

[Niohuruzh]

Hi, I use the current DeepTE with the command DeepTE.py -d deepwork/ -o deepTEout/ -i all.families.fa -sp F -m_dir /home/data but there is still the same problem:

Using TensorFlow backend. start time is 1675818480.4031475 Step1: transfer fasta data to CNN input data Step2: classify TEs Step2: 2) domain information is not exist Traceback (most recent call last): File "/media/leigod/f83cb121-4d63-4d87-8adf-a7bdefb24a63/home/leigod/software/DeepTE/DeepTE.py", line 274, in main() File "/media/leigod/f83cb121-4d63-4d87-8adf-a7bdefb24a63/home/leigod/software/DeepTE/DeepTE.py", line 249, in main pipeline_no_m.classify_pipeline(model_dir, input_CNN_data_file, temp_store_opt_dir, sp_type,te_fam,prop_thr) File "/media/leigod/f83cb121-4d63-4d87-8adf-a7bdefb24a63/home/leigod/software/DeepTE/scripts/DeepTE_pipeline_no_modification.py", line 307, in classify_pipeline model_nm = mt.group(1) AttributeError: 'NoneType' object has no attribute 'group'

What's wrong with my input data or environment? Looking forward your reply!

[yanhaidong1]

Hey Niohuruzh,

Would you mind checking again if /home/data contain all the models you downloaded from the links attached in this github? looks like tool cannot find the model files.

Best wishes, Haidong

[Niohuruzh]

Hi Haidong, Thanks for your quick reply. My dataset pwd is

/media/data/Fungi_model.tar.gz

Should I decompress the file or just use -m_dir /media/data/Fungi_model.tar.gz ？

[yanhaidong1]

Hey Niohuruzh,

Just decompress the file in your directory '/media/data/', under this directory, there are eight 'h5' format files if you decompress it correctly. Next use '-m_dir /media/data/'. I recommend you can also put all the h5 format files into a new directory like /media/F_models/ to run the tool based on '-m_dir /media/F_models/'

Best wishes, Haidong

[Niohuruzh]

Hi Haidong, It works now. Thanks for your advice!