dkoppstein
commented
4 years ago This should be fixable by updating tensorflow to the latest nightly. Here is the fix in tensorflow.
Open ChaoTang-SCU opened 4 years ago
dkoppstein
commented
4 years ago This should be fixable by updating tensorflow to the latest nightly. Here is the fix in tensorflow.
2020-06-22 20:41:02,717 == Analysis settings ====================================== 2020-06-22 20:41:02,717 Input: /mnt/raid62/BetaCoV/RawData/20200620/20200620_0916_MN27328_FAM92901_ea10d670/fast5_pass/ 2020-06-22 20:41:02,717 Output: /mnt/raid62/BetaCoV/Person/tangchao/analysis/DrictRNA/Poreplex/output 2020-06-22 20:41:02,717 Processes: 2 2020-06-22 20:41:02,717 Presets: rna-r941.cfg 2020-06-22 20:41:02,717 Basecall on-the-fly: No (use previous analyses) 2020-06-22 20:41:02,717 Trim 3' adapter: Yes 2020-06-22 20:41:02,717 Filter concatenated read: No 2020-06-22 20:41:02,717 Separate by barcode: Yes 2020-06-22 20:41:02,717 Real-time alignment: No 2020-06-22 20:41:02,717 FASTQ in output: Yes 2020-06-22 20:41:02,717 FAST5 in output: Yes 2020-06-22 20:41:02,717 Basecall table in output: No 2020-06-22 20:41:02,717 =========================================================== 2020-06-22 20:41:02,717 2020-06-22 20:48:57,596 [signal_analyzer.py:48] Unhandled exception AttributeError: 'list' object has no attribute 'items' 2020-06-22 20:48:57,596 Traceback (most recent call last): 2020-06-22 20:48:57,596 File "/home/tangchao/.pyenv/versions/3.7.4/lib/python3.7/site-packages/poreplex/signal_analyzer.py", line 48, in process_batch 2020-06-22 20:48:57,597 with SignalAnalyzer(config, batchid) as analyzer: 2020-06-22 20:48:57,597 File "/home/tangchao/.pyenv/versions/3.7.4/lib/python3.7/site-packages/poreplex/signal_analyzer.py", line 72, in init 2020-06-22 20:48:57,597 WorkerPersistenceStorage(config).retrieve_objects(self) 2020-06-22 20:48:57,597 File "/home/tangchao/.pyenv/versions/3.7.4/lib/python3.7/site-packages/poreplex/worker_persistence.py", line 48, in retrieve_objects 2020-06-22 20:48:57,597 storage = self.init_persistence_objects(self.config) 2020-06-22 20:48:57,597 File "/home/tangchao/.pyenv/versions/3.7.4/lib/python3.7/site-packages/poreplex/worker_persistence.py", line 83, in init_persistence_objects 2020-06-22 20:48:57,597 storage['loader'] = SignalLoader(config['signal_processing'], config['inputdir']) 2020-06-22 20:48:57,597 File "/home/tangchao/.pyenv/versions/3.7.4/lib/python3.7/site-packages/poreplex/signal_loader.py", line 41, in init 2020-06-22 20:48:57,597 self.scaler_model, self.scaler_cfg = self.load_scaler_model() 2020-06-22 20:48:57,597 File "/home/tangchao/.pyenv/versions/3.7.4/lib/python3.7/site-packages/poreplex/signal_loader.py", line 75, in load_scaler_model 2020-06-22 20:48:57,597 return keras.models.load_model(model_file), scaler_cfg 2020-06-22 20:48:57,597 File "/home/tangchao/.pyenv/versions/3.7.4/lib/python3.7/site-packages/tensorflow/python/keras/saving/save.py", line 180, in load_model 2020-06-22 20:48:57,597 return hdf5_format.load_model_from_hdf5(filepath, custom_objects, compile) 2020-06-22 20:48:57,597 File "/home/tangchao/.pyenv/versions/3.7.4/lib/python3.7/site-packages/tensorflow/python/keras/saving/hdf5_format.py", line 178, in load_model_from_hdf5 2020-06-22 20:48:57,597 custom_objects=custom_objects) 2020-06-22 20:48:57,597 File "/home/tangchao/.pyenv/versions/3.7.4/lib/python3.7/site-packages/tensorflow/python/keras/saving/model_config.py", line 55, in model_from_config 2020-06-22 20:48:57,597 return deserialize(config, custom_objects=custom_objects) 2020-06-22 20:48:57,597 File "/home/tangchao/.pyenv/versions/3.7.4/lib/python3.7/site-packages/tensorflow/python/keras/layers/serialization.py", line 174, in deserialize 2020-06-22 20:48:57,598 printable_module_name='layer') 2020-06-22 20:48:57,598 File "/home/tangchao/.pyenv/versions/3.7.4/lib/python3.7/site-packages/tensorflow/python/keras/utils/generic_utils.py", line 338, in deserialize_keras_object 2020-06-22 20:48:57,598 config, module_objects, custom_objects, printable_module_name) 2020-06-22 20:48:57,598 File "/home/tangchao/.pyenv/versions/3.7.4/lib/python3.7/site-packages/tensorflow/python/keras/utils/generic_utils.py", line 300, in class_and_config_for_serialized_keras_object 2020-06-22 20:48:57,598 for key, item in cls_config.items(): 2020-06-22 20:48:57,598 AttributeError: 'list' object has no attribute 'items' 2020-06-22 20:48:58,899 Finished.