Re: Model_selection problems -- November 12, 2008 - 18:48

Hi,

This seems like another bug.  Could you create a bug report for this?
> From your description, I should be able to easily modify the system
test added for you other bug report (https://gna.org/bugs/?12582) to
catch this one.  Oh, did you use the --debug command line argument to
produce this error message?

Cheers,

Edward


On Wed, Nov 12, 2008 at 6:36 PM, Brosey, Chris A
<chris.a.brosey@xxxxxxxxxxxxxx> wrote:
> Greetings,
>
> 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.
>
>
>
>
>
>
>
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