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choderalab
YANK analyze error
I am trying to run yank analyze after finishing my simulation successfully but i am facing errors.
with yank analyze --store={experiments} command it says:
(base) arma@UB:/media/arma/DATA/YANK_NEW_TRY/HIT1-explicit-output/experiments$ yank analyze --store=/media/arma/DATA/YANK_NEW_TRY/HIT1-explicit-output/experiments
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Traceback (most recent call last):
File "/home/arma/miniconda3/bin/yank", line 10, in
And while running the command for notebook yank analyze report --store={experiments} --output={mynotebook.ipynb} it gives following error:
(base) arma@UB:~$ yank analyze report --store=/media/arma/DATA/YANK_NEW_TRY/HIT1-explicit-output/experiments --output=mynotebook.ipynb
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Rendering notebook as a .ipynb file...
Processing notebook now, this may take a while...
Traceback (most recent call last):
File "/home/arma/miniconda3/bin/yank", line 10, in
sys.exit(main())
File "/home/arma/miniconda3/lib/python3.8/site-packages/yank/cli.py", line 73, in main
dispatched = getattr(commands, command).dispatch(command_args)
File "/home/arma/miniconda3/lib/python3.8/site-packages/yank/commands/analyze.py", line 123, in dispatch
return dispatch_report(args)
File "/home/arma/miniconda3/lib/python3.8/site-packages/yank/commands/analyze.py", line 322, in dispatch_report
run_notebook(store, output, notebook_serial_file, **analyzer_kwargs)
File "/home/arma/miniconda3/lib/python3.8/site-packages/yank/commands/analyze.py", line 281, in run_notebook
processed_notebook, resources = ep.preprocess(loaded_notebook, resource_data)
File "/home/arma/miniconda3/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 84, in preprocess
self.preprocess_cell(cell, resources, index)
File "/home/arma/miniconda3/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 105, in preprocess_cell
cell = self.execute_cell(cell, index, store_history=True)
File "/home/arma/miniconda3/lib/python3.8/site-packages/nbclient/util.py", line 84, in wrapped
return just_run(coro(*args, **kwargs))
File "/home/arma/miniconda3/lib/python3.8/site-packages/nbclient/util.py", line 62, in just_run
return loop.run_until_complete(coro)
File "/home/arma/miniconda3/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete
return future.result()
File "/home/arma/miniconda3/lib/python3.8/site-packages/nbclient/client.py", line 846, in async_execute_cell
self._check_raise_for_error(cell, exec_reply)
File "/home/arma/miniconda3/lib/python3.8/site-packages/nbclient/client.py", line 748, in _check_raise_for_error
raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
from matplotlib import pyplot as plt from yank.reports import notebook %matplotlib inline report = notebook.HealthReportData(store_directory, **analyzer_kwargs) report.report_version()
TypeError Traceback (most recent call last)
Input In [2], in
File ~/miniconda3/lib/python3.8/site-packages/yank/analyze.py:299, in ExperimentAnalyzer.init(self, store_directory, **analyzer_kwargs) 297 raise RuntimeError(err_msg) 298 with open(analysis_script_path, 'r') as f: --> 299 analysis = yaml.load(f) 300 phases_names = [] 301 signs = {}
TypeError: load() missing 1 required positional argument: 'Loader' TypeError: load() missing 1 required positional argument: 'Loader'
Update: this error was solved by changing yaml.load(f) into yaml.safe_load(f).
Now after running the script the error is with pymbar which is : pymbar.utils.ParameterError: Warning: Should have \sum_n W_nk = 1. Actual column sum for state 0 was 1.247458. 27 other columns have similar problems
