DNABERT
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running DNABERT pretrain.py file output environment error
Hi there,
I am running the DNABERT pretrain.py as instructed by the readme file, once it worked well and started the model training, while when I re-build the environment after a week, the system output the error as below:
08/30/2021 21:23:17 - WARNING - main - Process rank: -1, device: cpu, n_gpu: 0, distributed training: False, 16-bits training: False Traceback (most recent call last): File "/home/wuchao/dl/DNABERT/src/transformers/configuration_utils.py", line 225, in get_config_dict raise EnvironmentError OSError
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "run_pretrain.py", line 885, in
Not only for the terminal training version, but also for the google colab version, may I ask if anyone could help me solve this issue?
Thanks a lot!
Best regards, Chao
Your error message is the exact same one I got when I ran the model. Did you get the solution after that?
I figured it out what was causing the problem. It was just because I didn't change the path 'PATH_TO_DNABERT_REPO' in the line 'export SOURCE=PATH_TO_DNABERT_REPO'! Perhaps I didn't read the lines carefully. So changing the path into the real path solved the problem and it started training. I guess you already figured it out but I am just writing here to help someone who experiences a similar issue.
Hi there,
I figured it out on google colab, not our local machine.
Best regards, Chao
I have same problem on google colab, anyone can help?
I replaced
./content/drive/MyDrive/DNABERT/examples/sample_data/ft/6
with
/content/drive/MyDrive/DNABERT/examples/sample_data/ft/6
and it predicts well.