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error :replicating biobert exactly with NCbI dataset #190
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used tenforflow 1.15.2 as per instruction in requirement.txt C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\absl\flags_validators.py:206: UserWarning: Flag --task_name has a non-None default value; therefore, mark_flag_as_required will pass even if flag is not specified in the command line! WARNING:tensorflow:From C:\Users\Ayodee\biobert\run_ner.py:466: The name tf.logging.set_verbosity is deprecated. Please use tf.compat.v1.logging.set_verbosity instead. W0724 16:58:51.533188 12640 module_wrapper.py:139] From C:\Users\Ayodee\biobert\run_ner.py:466: The name tf.logging.set_verbosity is deprecated. Please use tf.compat.v1.logging.set_verbosity instead. WARNING:tensorflow:From C:\Users\Ayodee\biobert\run_ner.py:466: The name tf.logging.INFO is deprecated. Please use tf.compat.v1.logging.INFO instead. W0724 16:58:51.534185 12640 module_wrapper.py:139] From C:\Users\Ayodee\biobert\run_ner.py:466: The name tf.logging.INFO is deprecated. Please use tf.compat.v1.logging.INFO instead. WARNING:tensorflow:From C:\Users\Ayodee\biobert\modeling.py:92: The name tf.gfile.GFile is deprecated. Please use tf.io.gfile.GFile instead. W0724 16:58:51.534185 12640 module_wrapper.py:139] From C:\Users\Ayodee\biobert\modeling.py:92: The name tf.gfile.GFile is deprecated. Please use tf.io.gfile.GFile instead. Traceback (most recent call last): ; No such process |
Hello, pls i tried to replicate the trainig as specified aand using same NCIB dataset buut got stalked here .
this code line"
$ python run_ner.py --do_train=true --do_eval=true --vocab_file=$BIOBERT_DIR/vocab.txt --bert_config_file=$BIOBERT_DIR/bert_config.json --init_checkpoint=$BIOBERT_DIR/model.ckpt-1000000 --num_train_epochs=10.0 --data_dir=$NER_DIR --output_dir=$OUTPUT_DIr "
(tf15) C:\Users\Ayodee\biobert>python run_ner.py --do_train=true --do_eval=true --vocab_file$BIOBERT_DIR/vocab.txt --bert_config_file=BIOBERT_DIR/bert_config.json --init_checkpoint=BIOBERT_DIR/model.ckpt-1000000 --num_train_epochs=10.0 --data_dir=NER_DIR --output_dir=OUTPUT_DIR
WARNING:tensorflow:From C:\Users\Ayodee\biobert\optimization.py:87: The name tf.train.Optimizer is deprecated. Please use tf.compat.v1.train.Optimizer instead.
C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\absl\flags_validators.py:206: UserWarning: Flag --task_name has a non-None default value; therefore, mark_flag_as_required will pass even if flag is not specified in the command line!
'command line!' % flag_name)
WARNING:tensorflow:From run_ner.py:651: The name tf.app.run is deprecated. Please use tf.compat.v1.app.run instead.
Traceback (most recent call last):
File "run_ner.py", line 651, in
tf.app.run()
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\tensorflow_core\python\platform\app.py", line 40, in run
_run(main=main, argv=argv, flags_parser=_parse_flags_tolerate_undef)
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\absl\app.py", line 306, in run
flags_parser,
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\absl\app.py", line 375, in _run_init
flags_parser=flags_parser,
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\absl\app.py", line 220, in _register_and_parse_flags_with_usage
args_to_main = flags_parser(original_argv)
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\tensorflow_core\python\platform\app.py", line 31, in _parse_flags_tolerate_undef
return flags.FLAGS(_sys.argv if argv is None else argv, known_only=True)
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\tensorflow_core\python\platform\flags.py", line 112, in call
return self.dict['__wrapped'].call(*args, **kwargs)
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\absl\flags_flagvalues.py", line 673, in call
self.validate_all_flags()
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\absl\flags_flagvalues.py", line 533, in validate_all_flags
self._assert_validators(all_validators)
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\absl\flags_flagvalues.py", line 568, in _assert_validators
raise _exceptions.IllegalFlagValueError('\n'.join(messages))
absl.flags._exceptions.IllegalFlagValueError: flag --vocab_file=None: Flag --vocab_file must have a value other than None.
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