FileNotFoundError: [Errno 2] No such file or directory: 'deepTEout//opt_DeepTE.txt'

[LI-zijian1]

hi， I'm having some trouble running the command below：python3 DeepTE.py -d deepwork -o deepTEout -i repeatmodeler_unknowns.fasta -sp M -m_dir M_models Using Theano backend. start time is 1679238562.9101396 Step1: transfer fasta data to CNN input data Step2: classify TEs Step2: 2) domain information is not exist Traceback (most recent call last): File ".../DeepTE-master/DeepTE.py", line 274, in main() File ".../DeepTE-master/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 ".../DeepTE-master/scripts/DeepTE_pipeline_no_modification.py", line 339, in classify_pipeline predict_te(model_file_dic[model_name], model_name, x_all_test_list, y_all_test_nm_list,input_spe_type,y_all_test_nm_list,prop_thr) File ".../DeepTE-master/scripts/DeepTE_pipeline_no_modification.py", line 210, in predict_te model = load_model(model) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/keras/engine/saving.py", line 419, in load_model model = _deserialize_model(f, custom_objects, compile) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/keras/engine/saving.py", line 225, in _deserialize_model model = model_from_config(model_config, custom_objects=custom_objects) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/keras/engine/saving.py", line 458, in model_from_config return deserialize(config, custom_objects=custom_objects) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/keras/layers/init.py", line 55, in deserialize printable_module_name='layer') File ".../anaconda3/envs/py36/lib/python3.6/site-packages/keras/utils/generic_utils.py", line 145, in deserialize_keras_object list(custom_objects.items()))) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/keras/engine/sequential.py", line 301, in from_config model.add(layer) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/keras/engine/sequential.py", line 165, in add layer(x) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/keras/engine/base_layer.py", line 431, in call self.build(unpack_singleton(input_shapes)) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/keras/layers/convolutional.py", line 141, in build constraint=self.kernel_constraint) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/keras/legacy/interfaces.py", line 91, in wrapper return func(*args, *kwargs) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/keras/engine/base_layer.py", line 249, in add_weight weight = K.variable(initializer(shape), File ".../anaconda3/envs/py36/lib/python3.6/site-packages/keras/initializers.py", line 218, in call dtype=dtype, seed=self.seed) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/keras/backend/theano_backend.py", line 2600, in random_uniform return rng.uniform(shape, low=minval, high=maxval, dtype=dtype) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/theano/sandbox/rng_mrg.py", line 872, in uniform rstates = self.get_substream_rstates(nstreams, dtype) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/theano/configparser.py", line 117, in res return f(args, **kwargs) File ".../envs/py36/lib/python3.6/site-packages/theano/sandbox/rng_mrg.py", line 779, in get_substream_rstates multMatVect(rval[0], A1p72, M1, A2p72, M2) File ".../envs/py36/lib/python3.6/site-packages/theano/sandbox/rng_mrg.py", line 62, in multMatVect [A_sym, s_sym, m_sym, A2_sym, s2_sym, m2_sym], o, profile=False) File ".../envs/py36/lib/python3.6/site-packages/theano/compile/function.py", line 317, in function output_keys=output_keys) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/theano/compile/pfunc.py", line 486, in pfunc output_keys=output_keys) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/theano/compile/function_module.py", line 1841, in orig_function fn = m.create(defaults) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/theano/compile/function_module.py", line 1715, in create input_storage=input_storage_lists, storage_map=storage_map) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/theano/gof/link.py", line 699, in make_thunk storage_map=storage_map)[:3] File ".../anaconda3/envs/py36/lib/python3.6/site-packages/theano/gof/vm.py", line 1091, in make_all impl=impl)) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/theano/gof/op.py", line 955, in make_thunk no_recycling) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/theano/gof/op.py", line 858, in make_c_thunk output_storage=node_output_storage) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/theano/gof/cc.py", line 1217, in make_thunk keep_lock=keep_lock) File ".../anaconda3/envs/py36/lib/python3.6/site-packages/theano/gof/cc.py", line 1157, in compile keep_lock=keep_lock) File "/.../anaconda3/envs/py36/lib/python3.6/site-packages/theano/gof/cc.py", line 1609, in cthunk_factory key = self.cmodule_key() File ".../envs/py36/lib/python3.6/site-packages/theano/gof/cc.py", line 1300, in cmodule_key c_compiler=self.c_compiler(), File ".../anaconda3/envs/py36/lib/python3.6/site-packages/theano/gof/cc.py", line 1379, in cmodulekey np.core.multiarray._get_ndarray_c_version()) AttributeError: ('The following error happened while compiling the node', DotModulo(A, s, m, A2, s2, m2), '\n', "module 'numpy.core.multiarray' has no attribute '_get_ndarray_c_version'")

I used the following：pip install --upgrade numpy pip install --upgrade theano

I run again to get： /anaconda3/envs/py36/lib/python3.6/site-packages/keras/utils/conv_utils.py:82: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result. return np.copy(kernel[slices]) WARNING (theano.tensor.blas): We did not find a dynamic library in the library_dir of the library we use for blas. If you use ATLAS, make sure to compile it with dynamics library. /public/home/liupingping/anaconda3/envs/py36/lib/python3.6/site-packages/keras/utils/conv_utils.py:82: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result. return np.copy(kernel[slices]) start time is 1679240808.7187843 Step1: transfer fasta data to CNN input data Step2: classify TEs Step2: 2) domain information is not exist Step3: generate final output Traceback (most recent call last): File "/public/home/liupingping/22lzj/usefultool/DeepTE-master/DeepTE.py", line 274, in main() File "/public/home/liupingping/22lzj/usefultool/DeepTE-master/DeepTE.py", line 254, in main combine_opt.extract_combine_infor(temp_store_opt_dir, output_dir,sp_type) File "/public/home/liupingping/22lzj/usefultool/DeepTE-master/scripts/DeepTE_combine_opt.py", line 251, in extract_combine_infor with open (input_opt_combine_DeepTE_dir + '/opt_DeepTE.txt','w+') as opt: FileNotFoundError: [Errno 2] No such file or directory: 'deepTEout//opt_DeepTE.txt'

[LI-zijian1]

hi， Although I don't know what the reason is, I think I solved my problem, just remove this from the command:-o deepTEout

[songliVT]

Thank you for your email. I am glad that you find out a way to make this work.

Song

On Mon, Mar 20, 2023 at 3:01 AM LI-zijian1 @.***> wrote:

hi， Although I don't know what the reason is, I think I solved my problem, just remove this from the command:-o deepTEout

— Reply to this email directly, view it on GitHub https://github.com/LiLabAtVT/DeepTE/issues/22#issuecomment-1475717436, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACEEENR6SFNI3NSJ3VGCGV3W476EBANCNFSM6AAAAAAWADMLSE . You are receiving this because you are subscribed to this thread.Message ID: @.***>

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