PermissionError: [Errno 13] Permission denied

[gabrielrfernandes]

I used DeepVirFinder many times before, but suddenly it is running into an error. I removed the conda enviroment and installed again, but the error persists. Here is the output:

`python dvf.py -i /home/gabrielfernandes/tools/DeepVirFinder/test/crAssphage.fa -o /home/gabrielfernandes/tools/DeepVirFinder/teste/ -c 10

1. Loading Models. model directory /home/gabrielfernandes/tools/DeepVirFinder/models 2020-07-31 12:57:39.613175: I tensorflow/core/platform/cpu_feature_guard.cc:143] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 FMA 2020-07-31 12:57:39.645270: I tensorflow/core/platform/profile_utils/cpu_utils.cc:102] CPU Frequency: 2297270000 Hz 2020-07-31 12:57:39.648272: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x564fe738dd10 initialized for platform Host (this does not guarantee that XLA will be used). Devices: 2020-07-31 12:57:39.648302: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version 2020-07-31 12:57:39.648400: I tensorflow/core/common_runtime/process_util.cc:147] Creating new thread pool with default inter op setting: 2. Tune using inter_op_parallelism_threads for best performance. /home/gabrielfernandes/miniconda2/envs/dvf/lib/python3.6/site-packages/tensorflow/python/keras/utils/conv_utils.py:233: 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:tensorflow:Error in loading the saved optimizer state. As a result, your model is starting with a freshly initialized optimizer. WARNING:tensorflow:Error in loading the saved optimizer state. As a result, your model is starting with a freshly initialized optimizer. WARNING:tensorflow:Error in loading the saved optimizer state. As a result, your model is starting with a freshly initialized optimizer. WARNING:tensorflow:Error in loading the saved optimizer state. As a result, your model is starting with a freshly initialized optimizer.
2. Encoding and Predicting Sequences. processing line 1 processing line 1389 Traceback (most recent call last): File "dvf.py", line 211, in pool = multiprocessing.Pool(core_num) File "/home/gabrielfernandes/miniconda2/envs/dvf/lib/python3.6/multiprocessing/context.py", line 119, in Pool context=self.get_context()) File "/home/gabrielfernandes/miniconda2/envs/dvf/lib/python3.6/multiprocessing/pool.py", line 156, in init self._setup_queues() File "/home/gabrielfernandes/miniconda2/envs/dvf/lib/python3.6/multiprocessing/pool.py", line 249, in _setup_queues self._inqueue = self._ctx.SimpleQueue() File "/home/gabrielfernandes/miniconda2/envs/dvf/lib/python3.6/multiprocessing/context.py", line 112, in SimpleQueue return SimpleQueue(ctx=self.get_context()) File "/home/gabrielfernandes/miniconda2/envs/dvf/lib/python3.6/multiprocessing/queues.py", line 315, in init self._rlock = ctx.Lock() File "/home/gabrielfernandes/miniconda2/envs/dvf/lib/python3.6/multiprocessing/context.py", line 67, in Lock return Lock(ctx=self.get_context()) File "/home/gabrielfernandes/miniconda2/envs/dvf/lib/python3.6/multiprocessing/synchronize.py", line 162, in init SemLock.init(self, SEMAPHORE, 1, 1, ctx=ctx) File "/home/gabrielfernandes/miniconda2/envs/dvf/lib/python3.6/multiprocessing/synchronize.py", line 59, in init unlink_now) PermissionError: [Errno 13] Permission denied`

[jessieren]

Hi there,

Sorry for my late response. It is possible that the error was due to the version of Keras changes overtime. Could you please reinstall the packages following the exact versions of keras, theano, and python:

conda create --name dvf python=3.6 numpy theano=1.0.3 keras=2.2.4 scikit-learn Biopython h5py source activate dvf

Thanks.