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FreshAirTonight / af2complex

Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.
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Error finding features #20

Closed cassie-sims closed 1 year ago

cassie-sims commented 1 year ago

I get this error when running the run_af2comp.sh script.

could not locate feature input file under features/

I have made a file named 'features' within which are files with the proteins names as in the .lst file, and features generated using the run_fea_gen.sh script.

My .lst file reads as follows:

Target(components) Size(AAs) Name(for output)

PXYLORCO:2/PXYLOR1:2 1790 PXLY22

There are two folders in 'features' PXYLOR1 PXYLORCO

within each file is a features.pkl and .fas file.

FreshAirTonight commented 1 year ago

The python run script looks for feature pickle files under $fea_dir/$monomer_name. In run_af2comp.sh, the default $fea_dir is af2c_fea. Try place your feature folders, PXYLOR1 and PXYLORCO, under af2c_fea as subfolders. Or change the location of $fea_dir to point it to the correct path that has PXYLOR1 and PXYLORCO as subfolders.

cassie-sims commented 1 year ago

Hi! I realise it was because I specified the $fea_dir name in a way the python files in af2complex couldnt find it from their location. Fixed now. Thank you for a quick response :)

Cassie