Train BERT with CLI commands
I have downloaded the HuggingFace BERT model from the transformer repository found [here][1] and would like to train the model on custom NER labels by using the run_ner.py script as it is referenced [here][2] in the section "Named Entity Recognition".

I define model ("bert-base-german-cased"), data_dir ("Data/sentence_data.txt") and labels ("Data/labels.txt)" as defaults in the code.

Now I'm using this input for the command line:

```
python run_ner.py --output_dir="Models" --num_train_epochs=3 --logging_steps=100 --do_train --do_eval --do_predict
```

But all it does is telling me: 

```
Some weights of the model checkpoint at bert-base-german-cased were not used when initializing BertForTokenClassification: ['cls.predictions.bias', 'cls.predictions.transform.dense.weight', 'cls.predictions.transform.dense.bias', 'cls.predictions.transform.LayerNorm.w
eight', 'cls.predictions.transform.LayerNorm.bias', 'cls.predictions.decoder.weight', 'cls.seq_relationship.weight', 'cls.seq_relationship.bias']
- This IS expected if you are initializing BertForTokenClassification from the checkpoint of a model trained on another task or with another architecture (e.g. initializing a BertForSequenceClassification model from a BertForPretraining model).
- This IS NOT expected if you are initializing BertForTokenClassification from the checkpoint of a model that you expect to be exactly identical (initializing a BertForSequenceClassification model from a BertForSequenceClassification model).
Some weights of BertForTokenClassification were not initialized from the model checkpoint at bert-base-german-cased and are newly initialized: ['classifier.weight', 'classifier.bias']
You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference.
```

After that it just stops, not ending the script, but simply waiting. 

Does anyone know what could be the problem here? Am I missing a parameter?

My sentence_data.txt in CoNLL format looks like this (small snippet):
```
Strafverfahren O
gegen O
; O
wegen O
Diebstahls O
hat O
das O
Amtsgericht Ort
Leipzig Ort
- O
Strafrichter O
```
And that's how I defined my labels in labels.txt:
```
"Date", "Delikt", "Strafe_Tatbestand", "Schadensbetrag", "Geständnis_ja", "Vorstrafe_ja", "Vorstrafe_nein", "Ort",
"Strafe_Gesamtfreiheitsstrafe_Dauer", "Strafe_Gesamtsatz_Dauer", "Strafe_Gesamtsatz_Betrag"
```


  [1]: https://github.com/huggingface/transformers
  [2]: https://huggingface.co/transformers/task_summary.html
It's probably tokenizing. How big is your dataset?<|||||>This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.
