sup_all_atm.pdb is not created

[imerelli]

Hi, while training the modeling, I always get this error (each time with a different pdb file). As far as I understand, the TMP directory is created and the original pdb file is moved there, but then the *sup_all_atm.pdb is not created. Can you help me? Ivan

Epoch 0: 0%| | 0/203 [00:00<?, ?it/s] Traceback (most recent call last): File "/opt/tools/deg/PreMut/src/train.py", line 48, in training.fit(model_name='egnn') File "/opt/tools/deg/PreMut/src/train.py", line 43, in fit self.trainer.fit(model=lit_module,datamodule=datamodule) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/trainer/trainer.py", line 582, in fit call._call_and_handle_interrupt( File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/trainer/call.py", line 38, in _call_and_handle_interrupt return trainer_fn(*args, kwargs) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/trainer/trainer.py", line 624, in _fit_impl self._run(model, ckpt_path=self.ckpt_path) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/trainer/trainer.py", line 1061, in _run results = self._run_stage() File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/trainer/trainer.py", line 1140, in _run_stage self._run_train() File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/trainer/trainer.py", line 1163, in _run_train self.fit_loop.run() File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/loops/loop.py", line 199, in run self.advance(*args, *kwargs) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/loops/fit_loop.py", line 267, in advance self._outputs = self.epoch_loop.run(self._data_fetcher) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/loops/loop.py", line 199, in run self.advance(args, kwargs) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/loops/epoch/training_epoch_loop.py", line 214, in advance batch_output = self.batch_loop.run(kwargs) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/loops/loop.py", line 199, in run self.advance(*args, kwargs) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/loops/batch/training_batch_loop.py", line 88, in advance outputs = self.optimizer_loop.run(optimizers, kwargs) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/loops/loop.py", line 199, in run self.advance(*args, *kwargs) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/loops/optimization/optimizer_loop.py", line 200, in advance result = self._run_optimization(kwargs, self._optimizers[self.optim_progress.optimizer_position]) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/loops/optimization/optimizer_loop.py", line 247, in _run_optimization self._optimizer_step(optimizer, opt_idx, kwargs.get("batch_idx", 0), closure) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/loops/optimization/optimizer_loop.py", line 357, in _optimizer_step self.trainer._call_lightning_module_hook( File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/trainer/trainer.py", line 1305, in _call_lightning_module_hook output = fn(args, kwargs) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/core/module.py", line 1661, in optimizer_step optimizer.step(closure=optimizer_closure) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/core/optimizer.py", line 169, in step step_output = self._strategy.optimizer_step(self._optimizer, self._optimizer_idx, closure, kwargs) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/strategies/strategy.py", line 234, in optimizer_step return self.precision_plugin.optimizer_step( File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/plugins/precision/precision_plugin.py", line 121, in optimizer_step return optimizer.step(closure=closure, kwargs) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/torch/optim/optimizer.py", line 113, in wrapper return func(*args, kwargs) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/torch/autograd/grad_mode.py", line 27, in decorate_context return func(*args, *kwargs) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/torch/optim/adam.py", line 118, in step loss = closure() File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/plugins/precision/precision_plugin.py", line 107, in _wrap_closure closure_result = closure() File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/loops/optimization/optimizer_loop.py", line 147, in call self._result = self.closure(args, kwargs) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/loops/optimization/optimizer_loop.py", line 133, in closure step_output = self._step_fn() File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/loops/optimization/optimizer_loop.py", line 406, in _training_step training_step_output = self.trainer._call_strategy_hook("training_step", kwargs.values()) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/trainer/trainer.py", line 1443, in _call_strategy_hook output = fn(args, *kwargs) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/pytorch_lightning/strategies/strategy.py", line 378, in training_step return self.model.training_step(args, **kwargs) File "/opt/tools/deg/PreMut/src/LitModule.py", line 259, in training_step return self.step(batch,batch_idx,state='train') File "/opt/tools/deg/PreMut/src/LitModule.py", line 199, in step graph, label, info = self.prepare_graph(batch=batch,state=state) File "/opt/tools/deg/PreMut/src/LitModule.py", line 134, in prepare_graph graph, label_coords = pdb_reader.pdb_to_graph() File "/opt/tools/deg/PreMut/src/PDB_all_atom.py", line 529, in pdb_to_graph node_coords, label_coords = self.get_xyz() File "/opt/tools/deg/PreMut/src/PDB_all_atom.py", line 257, in get_xyz wild_df, mutant_df = self.do_TMalign(wild_ppdb=wild_ppdb,mutant_ppdb=mutant_ppdb) File "/opt/tools/deg/PreMut/src/PDB_all_atom.py", line 242, in do_TMalign pdb = PandasPdb().readpdb('TMP/{0}{1}.sup_all_atm.pdb'.format(self.wild_pdb,self.mutant_pdb)) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/biopandas/pdb/pandas_pdb.py", line 94, in read_pdb self.pdb_path, self.pdb_text = self._read_pdb(path=path) File "/opt/tools/deg/miniforge3/envs/PreMut/lib/python3.10/site-packages/biopandas/pdb/pandas_pdb.py", line 316, in _read_pdb with openf(path, r_mode) as f: FileNotFoundError: [Errno 2] No such file or directory: 'TMP/1ire_7w8m.sup_all_atm.pdb'

[sajidmahmud]

Hello, Could you check if you have installed TMalign? It is required for the training portion.