No output after running train_segmentation.py about deeppocket HOT 6 CLOSED

Hi, thanks, I've figured out how to fix that particular error. Had to re-download the original scPDB dataset and extract all the cavity6.mol2 files from there.

I have a follow-up question - How do I read .molcache2 files? I can't find any documentation regarding .molcache2 files online and I want to read the "scPDB_new.molcache2" file. Accessing .mol2 files is simple enough, but I can't seem to find anything for .molcache2 files.

from deeppocket.

I have a slight suspicion this is a wandb issue, have you tried changing its version and retrying? Have you downloaded the scpdb dataset for the cavity files? You could also check the local repository of the wandb and see if theres some data being saved there. If you share the colab link I could try reproducing it

from deeppocket.

Thanks for the suggestions!
I tried changing the wandb version, going back till 0.14.0, no change. Nothing in the wandb repositories as well. It shows that the program just runs and crashes although there's no error output (from what I can see) which is very baffling.

I downloaded the 3.5GB compressed scPDB dataset from the original site, but I'm not sure how to extract the cavity6.mol2 files specifically from that.

I'd be happy to share the Colab link, if you could send your email ID I can give access to the link.

from deeppocket.

If its getting killed without any errors it could also be a memory issue, try reducing the batch size?

from deeppocket.

Tried it, still crashed. On Colab, it shows the the cell executed in 20-30s without any errors (it should take far longer than that), while on wandb it shows the cell running for 7-8 minutes before crashing. I'm not sure what to make of it honestly.

I'll try re-downloading all relevant files from the repository again and trying again.

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molcache2 files are binary files, solely defined to be used by the program. Basically a compressed form of your pdb/mol files that would be quicker i/o

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