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1 Parent(s): 4d34264

stability structures and seq

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Files changed (5) hide show
  1. stability/esmfold_predictions.log +707 -0
  2. stability/predictions_test.tar.gz +3 -0
  3. stability/predictions_train.tar.gz +3 -0
  4. stability/stability_test.fasta +0 -0
  5. stability/stability_train.fasta +0 -0
stability/esmfold_predictions.log ADDED
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+ Starting predictions for training set...
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+ Total sequences: 53614
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+ Using 2 GPUs
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+ ~26807 sequences per GPU
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+ /home/tianyu/miniconda3/envs/esmfold/lib/python3.9/site-packages/lightning_fabric/__init__.py:29: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
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+ __import__("pkg_resources").declare_namespace(__name__)
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+ /home/tianyu/miniconda3/envs/esmfold/lib/python3.9/site-packages/lightning_fabric/__init__.py:29: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
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+ __import__("pkg_resources").declare_namespace(__name__)
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+ /home/tianyu/miniconda3/envs/esmfold/lib/python3.9/site-packages/openfold/utils/tensor_utils.py:92: UserWarning: Using a non-tuple sequence for multidimensional indexing is deprecated and will be changed in pytorch 2.9; use x[tuple(seq)] instead of x[seq]. In pytorch 2.9 this will be interpreted as tensor index, x[torch.tensor(seq)], which will result either in an error or a different result (Triggered internally at /pytorch/torch/csrc/autograd/python_variable_indexing.cpp:306.)
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+ return data[ranges]
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+ /home/tianyu/miniconda3/envs/esmfold/lib/python3.9/site-packages/openfold/utils/tensor_utils.py:92: UserWarning: Using a non-tuple sequence for multidimensional indexing is deprecated and will be changed in pytorch 2.9; use x[tuple(seq)] instead of x[seq]. In pytorch 2.9 this will be interpreted as tensor index, x[torch.tensor(seq)], which will result either in an error or a different result (Triggered internally at /pytorch/torch/csrc/autograd/python_variable_indexing.cpp:306.)
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+ return data[ranges]
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+ GPU 1: Progress 26800/26807
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+ GPU 1: Completed!
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+ All predictions completed!
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+ Starting predictions for test set...
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+ Total sequences: 12851
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+ Using 2 GPUs
561
+ ~6425 sequences per GPU
562
+ /home/tianyu/miniconda3/envs/esmfold/lib/python3.9/site-packages/lightning_fabric/__init__.py:29: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
563
+ __import__("pkg_resources").declare_namespace(__name__)
564
+ /home/tianyu/miniconda3/envs/esmfold/lib/python3.9/site-packages/lightning_fabric/__init__.py:29: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
565
+ __import__("pkg_resources").declare_namespace(__name__)
566
+ /home/tianyu/miniconda3/envs/esmfold/lib/python3.9/site-packages/openfold/utils/tensor_utils.py:92: UserWarning: Using a non-tuple sequence for multidimensional indexing is deprecated and will be changed in pytorch 2.9; use x[tuple(seq)] instead of x[seq]. In pytorch 2.9 this will be interpreted as tensor index, x[torch.tensor(seq)], which will result either in an error or a different result (Triggered internally at /pytorch/torch/csrc/autograd/python_variable_indexing.cpp:306.)
567
+ return data[ranges]
568
+ /home/tianyu/miniconda3/envs/esmfold/lib/python3.9/site-packages/openfold/utils/tensor_utils.py:92: UserWarning: Using a non-tuple sequence for multidimensional indexing is deprecated and will be changed in pytorch 2.9; use x[tuple(seq)] instead of x[seq]. In pytorch 2.9 this will be interpreted as tensor index, x[torch.tensor(seq)], which will result either in an error or a different result (Triggered internally at /pytorch/torch/csrc/autograd/python_variable_indexing.cpp:306.)
569
+ return data[ranges]
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+ GPU 0: Loading ESMFold model...
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+ GPU 0: Processing 6425 sequences (indices 0-6425)
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+ GPU 0: Completed!
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+ GPU 1: Loading ESMFold model...
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+ GPU 1: Processing 6426 sequences (indices 6425-12851)
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+ GPU 1: Completed!
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+ All predictions completed!
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+ All predictions completed!
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