Model_selection problemsModel_selection problemsGreetings,
I have encountered a second problem in attempting to run the full_analysis.py script under the latest version of relax (v1.3.2/repository 1.3). For some reason, I am generating a RelaxNoPipeError during execution of the model_selection function, specifically when model_selection.py attempts to duplicate and switch to the new ‘aic’ data pipe after processing the first residue (see output and traceback logs below). I have not altered any code within the full_analysis.py beyond that specified in the user variables and am running the script exclusively for models ‘tm0’ and ‘tm1.’ I have also used input data (R1, R2, and NOE files) from /test_suite/shared_data/model_free/S2…0.149, modified to include ‘None’ for absent data values of GLY1.
As always, I appreciate any help or suggestions you might have to offer. Enjoy a great morning!
Best regards,
Chris
Log File (edited)
relax> pipe.create(pipe_name='tm0', pipe_type='mf')
relax> sequence.read
Mol_name Res_num Res_name Spin_num Spin_name
None 1 GLY None None
None 2 ALA None N
relax> grid_search(lower=None, upper=None, inc=11, constraints=True, verbosity=1)
Fitting to spin ':2&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~
relax> results.write(file='results', dir='local_tm/tm0', force=True, compress_type=1)
Opening the file 'local_tm/tm0/results.bz2' for writing.
relax> pipe.create(pipe_name='tm1', pipe_type='mf')
relax> sequence.read
Mol_name Res_num Res_name Spin_num Spin_name
None 1 GLY None None
None 2 ALA None N
relax> grid_search(lower=None, upper=None, inc=11, constraints=True, verbosity=1)
Fitting to spin ':2&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~
relax> minimise(*args=('newton',), func_tol=1e-25, max_iterations=10000000, constraints=True, scaling=True, verbosity=1)
Fitting to spin ':2&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~
relax> results.write(file='results', dir='local_tm/tm1', force=True, compress_type=1)
Opening the file 'local_tm/tm1/results.bz2' for writing.
relax> eliminate(function=None, args=None)
relax> model_selection(method='AIC', modsel_pipe='aic', pipes=['tm0', 'tm1'])
AIC model selection.
Model-free model of spin ':1&:GLY@None'.
Data pipe Num_params_(k) Num_data_sets_(n) Chi2 Criterion
The model from the data pipe None has been selected.
relax> state.save(state='relax_state_20081211_101217', dir_name=None, force=False, compress_type=1)
Opening the file 'relax_state_20081211_101217.bz2' for writing.
Traceback Log
Traceback (most recent call last):
File "sample_scripts/full_analysis2.py", line 665, in <module>
Main(self.relax)
File "sample_scripts/full_analysis2.py", line 221, in __init__
self.model_selection(modsel_pipe='aic', dir=self.base_dir + 'aic')
File "sample_scripts/full_analysis2.py", line 600, in model_selection
model_selection(method='AIC', modsel_pipe=modsel_pipe, pipes=self.pipes)
File "/home/broseyca/relax/relax-1.3.2/relax-1.3/prompt/model_selection.py", line 132, in model_selection
model_selection.select(method=method, modsel_pipe=modsel_pipe, pipes=pipes)
File "/home/broseyca/relax/relax-1.3.2/relax-1.3/generic_fns/model_selection.py", line 298, in select
switch(modsel_pipe)
File "/home/broseyca/relax/relax-1.3.2/relax-1.3/generic_fns/pipes.py", line 230, in switch
test(pipe_name)
File "/home/broseyca/relax/relax-1.3.2/relax-1.3/generic_fns/pipes.py", line 256, in test
raise RelaxNoPipeError, pipe_name
RelaxNoPipeError: RelaxError: The data pipe 'aic' has not been created yet.