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kundajelab / chrombpnet

Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
https://github.com/kundajelab/chrombpnet/wiki
MIT License
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TFmodisco lite doesn't seem to run #175

Closed rb56 closed 10 months ago

rb56 commented 10 months ago

Hello,

I'm trying to run TFmodisco-lite on counts_scores.h5 file to carry out motif discovery. However, the command doesn't seem to run and no output or error is generated. The job ends due to Timeout of GPU resources.

This is the code I use to run TF modisco in the chrombpnet virtual environment modisco motifs -i new.CS.counts_scores.h5 -n 1000000 -o $wordir_path/$pred_prefix_modisco_results.h5 Is anyone facing the same error?

panushri25 commented 10 months ago

For modisco lite related help you can post here - https://github.com/jmschrei/tfmodisco-lite/

Modisco lite does not use GPU btw, If you can post the log or out that would be helpful for debugging