search

dohlee / chromoformer

The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
GNU General Public License v3.0
31 stars 2 forks source link

FileNotFoundError #2

Closed liuyq123 closed 2 years ago

liuyq123 commented 2 years ago

Hello, I got some errors when trying to retrain Chromoformer. I first downloaded and processed data with the pipeline provided in the preprocessing folder, and then ran train.py in the chromoformer folder. However, I got FileNotFoundError. Any ideas on how to fix it? Thanks.

dohlee commented 2 years ago

Sure. Could you please paste the full error message here? It would greatly help to diagnose the issue.

Thanks.

liuyq123 commented 2 years ago

Thank you so much! Here's the error message.

Screen Shot 2022-06-28 at 12 39 14 AM
dohlee commented 2 years ago

Thank you for your report. The problem was that preprocessing/scripts/extract_signals.py was generating wrong read depth signals for regions around TSS. I fixed preprocessing/scripts/extract_signals.py to resolve it.

Could you please remove the data directory under preprocessing directory, pull the current version of github repo (where extract_signals.py is fixed) and re-run the snakemake pipeline to generate correct .npy files? If the model training works fine with that, then I'll close this issue.

Thank you again for opening this issue, and please let me know whether it works or not.

liuyq123 commented 2 years ago

Thanks a lot for fixing the problem! It works well now.

dohlee commented 2 years ago

Good. Closing the issue.