This PR is stale because it has been open for 14 days with no activity.

as to 2:
currently, if not all queries are processed, the output will look something like this:

Graph/Query with ID residue-srv:A:78:Valine->Isoleucine:pdb5qip ran into an Exception and was not written to the hdf5 file.
Exception found: ValueError: Residue not found in data_raw/srv/pdb/pdb5qip.ent: A 78.
You may proceed with your analysis, but this query will be ignored.

Graph/Query with ID residue-srv:A:78:Valine->Isoleucine:pdb5qio ran into an Exception and was not written to the hdf5 file.
Exception found: ValueError: Residue not found in data_raw/srv/pdb/pdb5qio.ent: A 78.
You may proceed with your analysis, but this query will be ignored.

Graph/Query with ID residue-srv:A:20:Arginine->Tryptophan:pdb5qis ran into an Exception and was not written to the hdf5 file.
...
You may proceed with your analysis, but this query will be ignored.

Not all queries have been processed. You can proceed with the analysis of 53/72 queries.
Set log_error_traceback to True for advanced troubleshooting

previously, it looked like this:

Graph/Query with ID residue-srv:A:6:Phenylalanine->Cysteine:pdb1tff ran into an Exception (ValueError: Residue not found in data_raw/srv/pdb/pdb1tff.ent: A 6), and it has not been written to the hdf5 file. More details below:
Residue not found in data_raw/srv/pdb/pdb1tff.ent: A 6
Traceback (most recent call last):
File "/home/dbodor/git/DeepRank/deeprank2/deeprank2/query.py", line 460, in _process_one_query
graph = query.build(self._feature_modules)
File "/home/dbodor/git/DeepRank/deeprank2/deeprank2/query.py", line 192, in build
graph = self._build_helper()
File "/home/dbodor/git/DeepRank/deeprank2/deeprank2/query.py", line 275, in _build_helper
raise ValueError(msg)
ValueError: Residue not found in data_raw/srv/pdb/pdb1tff.ent: A 6

Graph/Query with ID residue-srv:A:91:Arginine->Histidine:pdb4zw9 ran into an Exception (ValueError: Residue not found in data_raw/srv/pdb/pdb4zw9.ent: A 91), and it has not been written to the hdf5 file. More details below:
Residue not found in data_raw/srv/pdb/pdb4zw9.ent: A 91
Traceback (most recent call last):
File "/home/dbodor/git/DeepRank/deeprank2/deeprank2/query.py", line 460, in _process_one_query
graph = query.build(self._feature_modules)
File "/home/dbodor/git/DeepRank/deeprank2/deeprank2/query.py", line 192, in build
graph = self._build_helper()
File "/home/dbodor/git/DeepRank/deeprank2/deeprank2/query.py", line 275, in _build_helper
raise ValueError(msg)
ValueError: Residue not found in data_raw/srv/pdb/pdb4zw9.ent: A 91

Graph/Query with ID residue-srv:A:227:Glutamine->Leucine:pdb4zw9 ran into an Exception (ValueError: Residue not found in data_raw/srv/pdb/pdb4zw9.ent: A 227), and it has not been written to the hdf5 file. More details below:
Residue not found in data_raw/srv/pdb/pdb4zw9.ent: A 227
...
graph = self._build_helper()
File "/home/dbodor/git/DeepRank/deeprank2/deeprank2/query.py", line 275, in _build_helper
raise ValueError(msg)
ValueError: Residue not found in data_raw/srv/pdb/pdb5qiz.ent: A 78