Ruben Alvarez

Ahhh, I see it now, thank you for that @ch4rr0. Running the code with --ignore-quals: `bowtie2 -x b2index -a -U singleq.fastq -q -5 32 -3 0 --end-to-end --norc --no-hd --ignore-quals...

@johnnytam100, I'm afraid this github has not been maintained in a long while. Even if an example was provided, you will still need to purge the code because it is...

@wjs20, did you get any further, by any chance?

@wjs20, a full broadsword thrust... Had to correct probably all the modules, eg the boolean arguments in Arguments.py, that are wrongly coded -very fun to ask for True and get...

Hi, I do not have access to my computer right now, but I can say that there are tons of problems. For one, check you arguments.py because you may not...

@orange2350, on top of that, the output of dmasif --search is embeddings, not a probability of binding like with --site, so you still need to figure out how to use...

The parameters are described here https://github.com/FreyrS/dMaSIF/blob/master/Arguments.py @dangraysf, thanks for pointing at the model too, very useful. Wished the github was mainainted, it took me a while to figure out the...

@orange2350, have you made any progress that you could share, by any chance? I am stuck at the point that I have the protein embeddings for protein pairs, but do...

@jeanfeydy, I wonder if you found the issue here? A workaround is to add torch.cuda.empty_cache() after each train/val/test within each epoch, but still memory creeps up a few Mb per...