Failing test in new installation

[erikedlund]

Thank you for publishing such a cool tool! I'm running into some issues installing and using the scoring function.

First, I'm seeing tests failing in a fresh installation:

FAILED tests/test_biowrappers.py::TestBioWrappers::test_depth_res - Failed: Unexpected success
=================================================== 1 failed, 21 passed, 3 xfailed, 144223 warnings in 347.77s (0:05:47) ================================================

DeepRank-GNN-esm_test.txt

When I attempt to use the model, an assertion error is thrown suggesting the embeddings are invalid:

$ deeprank-gnn-esm-predict ./053_5.pdb C A ../paper_pretrained_models/scoring_of_docking_models/gnn_esm/treg_yfnat_b64_e20_lr0.001_foldall_esm.pth.tar 2024-12-03 20:51:26,609 predict:60 INFO - Setting up workspace - /share/data/public/edlunde/git/DeepRank-GNN-esm/test/053_5-gnn_esm_pred_C_A 2024-12-03 20:51:26,616 predict:69 INFO - Renumbering PDB file. 2024-12-03 20:51:26,685 predict:112 INFO - Reading sequence of PDB 053_5.pdb 2024-12-03 20:51:26,716 predict:138 INFO - Generating embedding for protein sequence. 2024-12-03 20:51:26,716 predict:139 INFO - ################################################################################ 2024-12-03 20:51:33,577 predict:154 INFO - Read /share/data/public/edlunde/git/DeepRank-GNN-esm/test/053_5-gnn_esm_pred_C_A/all.fasta with 2 sequences 2024-12-03 20:51:33,586 predict:164 INFO - Processing 1 of 1 batches (2 sequences) 2024-12-03 20:51:43,586 predict:206 INFO - ################################################################################ 2024-12-03 20:51:43,669 predict:211 INFO - Generating graph, using 31 processors Graphs added to the HDF5 file Traceback (most recent call last): File "~/conda/envs/deeprank-gnn-esm-cpu-env/bin/deeprank-gnn-esm-predict", line 8, in <module> sys.exit(main()) File "~/conda/envs/deeprank-gnn-esm-cpu-env/lib/python3.9/site-packages/deeprank_gnn/predict.py", line 335, in main graph = create_graph(pdb_path=pdb_file.parent, workspace_path=workspace_path) File "~/conda/envs/deeprank-gnn-esm-cpu-env/lib/python3.9/site-packages/deeprank_gnn/predict.py", line 216, in create_graph GraphHDF5( File "~/conda/envs/deeprank-gnn-esm-cpu-env/lib/python3.9/site-packages/deeprank_gnn/GraphGenMP.py", line 141, in __init__ self._add_embedding(outfile=outfile, pdbs=pdbs, embedding_path=embedding_path) File "~/conda/envs/deeprank-gnn-esm-cpu-env/lib/python3.9/site-packages/deeprank_gnn/GraphGenMP.py", line 247, in _add_embedding assert not torch.all(torch.eq(embedding_tersor, 0)) AssertionError

I am running in CPU mode, for what it's worth, but the test failure seems unrelated.

[erikedlund]

I've discovered a workaround for the crash. My .pdb files are named with a unique convention. Renaming the files to a pattern matching the RCSB convention (e.g. 1XXX.pdb) allows DeepRank-GNN-esm to proceed.

[ntxxt]

Thank you for your interest in our tool!
Good work!

[erikedlund]

For the record, the first issue I reported here remains unsolved (the failing test).

[ntxxt]

Hi there,

In what part is the code failing? The assert check ensures embedding is added correctly to the graph.

If you re-name your pdb file as xxxx.pdb, the code should run fine. Also, try to use pdb_tidy command from pdb-tools to clean the pdb file if it is not the standard format.
I can also look at your input pdb file if you cannot identify the issue.

Best,
Xiaotong

[erikedlund]

This is the pytest test output from the installation instructions. I filed this as a single issue because I wondered if the test failure indicated the source of the problem with the file names but it seems like the assumption for their length is intended.

FAILED tests/test_biowrappers.py::TestBioWrappers::test_depth_res - Failed: Unexpected success
=================================================== 1 failed, 21 passed, 3 xfailed, 144223 warnings in 347.77s (0:05:47) ================================================

[erikedlund]

Here's the complete output of a test failure from a fresh installation on a new Ubuntu machine with a 4090.
DeepRank-GNN-esm-test-failures.txt

The main failure seems to be in TestBioWrappers.test_depth_res.

Let me know if there are any other logs I can provide.