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BioinfoMachineLearning / DIPS-Plus

The Enhanced Database of Interacting Protein Structures for Interface Prediction
https://zenodo.org/record/5134732
GNU General Public License v3.0
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about psaia #5

Closed XuBlack closed 3 years ago

XuBlack commented 3 years ago

When I use the command python3 project/datasets/builder/generate_psaia_features.py "/home/PSAIA_1.0_source/bin/linux/psa" ./project/datasets/builder/psaia_config_file_db5.txt ./project/datasets/DB5/raw ./project/datasets/DB5/interim/parsed ./project/datasets/DB5/interim/parsed ./project/datasets/DB5/interim/external_feats --source_type db5, the returned result is as follows:

Using backend: pytorch

2021-10-07 03:03:22,279 INFO 10046: Generating PSAIA features from PDB files in ./project/datasets/DB5/interim/parsed

2021-10-07 03:03:46,257 INFO 10046: 460 PDB files to process with PSAIA

2021-10-07 03:03:46,271 INFO 10046: Processing 1 inputs.

2021-10-07 03:03:46,272 INFO 10046: Sequential Mode.

2021-10-07 03:03:46,272 INFO 10046: PSAIA'ing ./project/datasets/DB5/interim/external_feats/PSAIA/DB5/pdb_list.fls

Traceback (most recent call last):

  File "project/datasets/builder/generate_psaia_features.py", line 49, in <module>

    main()

  File "/usr/local/lib/python3.6/dist-packages/click/core.py", line 764, in __call__

    return self.main(*args, **kwargs)

  File "/usr/local/lib/python3.6/dist-packages/click/core.py", line 717, in main

    rv = self.invoke(ctx)

  File "/usr/local/lib/python3.6/dist-packages/click/core.py", line 956, in invoke

    return ctx.invoke(self.callback, **ctx.params)

  File "/usr/local/lib/python3.6/dist-packages/click/core.py", line 555, in invoke

    return callback(*args, **kwargs)

  File "project/datasets/builder/generate_psaia_features.py", line 42, in main

    map_all_protrusion_indices(psaia_config, pdb_dataset, pkl_dataset, pruned_dataset, output_dir, source_type)

  File "/usr/local/lib/python3.6/dist-packages/atom3/conservation.py", line 364, in map_all_protrusion_indices

    par.submit_jobs(map_protrusion_indices, inputs, 1)  # PSAIA is inherently single-threaded in execution

  File "/usr/local/lib/python3.6/dist-packages/parallel.py", line 63, in submit_jobs

    out = [function(*args) for args in inputs]

  File "/usr/local/lib/python3.6/dist-packages/parallel.py", line 63, in <listcomp>

    out = [function(*args) for args in inputs]

  File "/usr/local/lib/python3.6/dist-packages/atom3/conservation.py", line 193, in map_protrusion_indices

    gen_protrusion_index(psaia_config_file, file_list_file)

  File "/usr/local/lib/python3.6/dist-packages/atom3/conservation.py", line 44, in gen_protrusion_index

    _psaia(psaia_config_file, file_list_file)

  File "/usr/local/lib/python3.6/dist-packages/atom3/conservation.py", line 253, in _psaia

    subprocess.check_call(command, shell=True, stderr=f_err, stdout=f_out)

  File "/usr/lib/python3.6/subprocess.py", line 311, in check_call

    raise CalledProcessError(retcode, cmd)

subprocess.CalledProcessError: Command 'yes y | psa ./project/datasets/builder/psaia_config_file_db5.txt 

./project/datasets/DB5/interim/external_feats/PSAIA/DB5/pdb_list.fls returned non-zero exit status 1.

Why does this happen?