Hi Mark! Welcome to the relax mailing lists. Sorry for the delayed response, I am currently on holidays. Please see below:
On Friday, 15 March 2019, Mark Bostock <[email protected]> wrote: > Dear all, > > I am new to using relax. I am currently trying to analyse some cpmg > relaxation dispersion data, however, whenever I try and run this I get the > following error: > > Exception raised in thread. > > Traceback (most recent call last): > File "/sbgrid/programs/x86_64-linux/relax/4.0.3/gui/analyses/execute.py", > line 87, in run > self.run_analysis() > File > "/sbgrid/programs/x86_64-linux/relax/4.0.3/gui/analyses/auto_relax_disp.py", > line 755, in run_analysis > Relax_disp(pipe_name=self.data.pipe_name, > pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir, > models=self.data.models, grid_inc=self.data.inc, > mc_sim_num=self.data.mc_sim_num, exp_mc_sim_num=self.data.exp_mc_sim_num, > pre_run_dir=self.data.pre_run_dir, > mc_sim_all_models=self.data.mc_sim_all_models, > insignificance=self.data.insignificance, numeric_only=self.data.numeric_only, > r1_fit=self.data.r1_fit) > File > "/sbgrid/programs/x86_64-linux/relax/4.0.3/auto_analyses/relax_disp.py", > line 137, in __init__ > self.run() > File > "/sbgrid/programs/x86_64-linux/relax/4.0.3/auto_analyses/relax_disp.py", > line 616, in run > self.optimise(model=model, model_path=model_path) > File > "/sbgrid/programs/x86_64-linux/relax/4.0.3/auto_analyses/relax_disp.py", > line 397, in optimise > self.interpreter.minimise.grid_search(inc=self.grid_inc) > File "/sbgrid/programs/x86_64-linux/relax/4.0.3/prompt/uf_objects.py", > line 225, in __call__ > self._backend(*new_args, **uf_kargs) > File "/sbgrid/programs/x86_64-linux/relax/4.0.3/pipe_control/minimise.py", > line 213, in grid_search > api.grid_search(lower=model_lower, upper=model_upper, inc=model_inc, > scaling_matrix=scaling_matrix, constraints=constraints, verbosity=verbosity) > File > "/sbgrid/programs/x86_64-linux/relax/4.0.3/specific_analyses/relax_disp/api.py", > line 621, in grid_search > self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc, > scaling_matrix=scaling_matrix, constraints=constraints, > verbosity=verbosity, sim_index=sim_index) > File > "/sbgrid/programs/x86_64-linux/relax/4.0.3/specific_analyses/relax_disp/api.py", > line 812, in minimise > minimise_r2eff(spins=spins, spin_ids=spin_ids, min_algor=min_algor, > min_options=min_options, func_tol=func_tol, grad_tol=grad_tol, > max_iterations=max_iterations, constraints=constraints, > scaling_matrix=scaling_matrix[model_index], verbosity=verbosity, > sim_index=sim_index, lower=lower_i, upper=upper_i, inc=inc_i) > File > "/sbgrid/programs/x86_64-linux/relax/4.0.3/specific_analyses/relax_disp/optimisation.py", > line 360, in minimise_r2eff > for exp_type, frq, offset, point in loop_exp_frq_offset_point(): > File > "/sbgrid/programs/x86_64-linux/relax/4.0.3/specific_analyses/relax_disp/data.py", > line 1344, in loop_exp_frq_offset_point > for point, di in loop_point(exp_type=exp_type, frq=frq, offset=offset, > return_indices=True): > File > "/sbgrid/programs/x86_64-linux/relax/4.0.3/specific_analyses/relax_disp/data.py", > line 1674, in loop_point > fields = return_cpmg_frqs_single(exp_type=exp_type, frq=frq, > offset=offset, time=time, ref_flag=ref_flag) > File > "/sbgrid/programs/x86_64-linux/relax/4.0.3/specific_analyses/relax_disp/data.py", > line 2854, in return_cpmg_frqs_single > if cdp.cpmg_frqs[id] != point: > KeyError: '500_reference' This seems to be a data set up error. But there is not enough information to reproduce or determine what happed. Are you able to create a bare minimum data set - e.g. a single spin system - that reproduces the error? This is easiest if the relax controller output is copied and pasted, and the line contents after each "relax> " instance used to create a basic script. If you are able to then create a bug report: https://sourceforge.net/p/nmr-relax/tickets/new/ And attach the data files (and a script if you create one), it would be much appreciated. Feel free to obfuscate, randomise, etc. the data as much as you wish, as long as the posted data triggers the error. Note that if I can reproduce the bug, in most cases I can have a fix within 5-10 min. Though I still have a few weeks of holidays left and cannot work on a fix until after I return. However, I'm not sure from the error logs what this error actually relates > to. > > In addition, if I try and make changes to the setup and rerun, I get the > error: > > Exception raised in thread. > > Traceback (most recent call last): > File "/sbgrid/programs/x86_64-linux/relax/4.0.3/gui/analyses/execute.py", > line 87, in run > self.run_analysis() > File > "/sbgrid/programs/x86_64-linux/relax/4.0.3/gui/analyses/auto_relax_disp.py", > line 755, in run_analysis > Relax_disp(pipe_name=self.data.pipe_name, > pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir, > models=self.data.models, grid_inc=self.data.inc, > mc_sim_num=self.data.mc_sim_num, exp_mc_sim_num=self.data.exp_mc_sim_num, > pre_run_dir=self.data.pre_run_dir, > mc_sim_all_models=self.data.mc_sim_all_models, > insignificance=self.data.insignificance, numeric_only=self.data.numeric_only, > r1_fit=self.data.r1_fit) > File > "/sbgrid/programs/x86_64-linux/relax/4.0.3/auto_analyses/relax_disp.py", > line 137, in __init__ > self.run() > File > "/sbgrid/programs/x86_64-linux/relax/4.0.3/auto_analyses/relax_disp.py", > line 600, in run > self.interpreter.pipe.copy(pipe_from=self.pipe_name, > pipe_to=model_pipe, bundle_to=self.pipe_bundle) > File "/sbgrid/programs/x86_64-linux/relax/4.0.3/prompt/uf_objects.py", > line 225, in __call__ > self._backend(*new_args, **uf_kargs) > File "/sbgrid/programs/x86_64-linux/relax/4.0.3/pipe_control/pipes.py", > line 191, in copy > raise RelaxPipeError(pipe_to) > RelaxPipeError: RelaxError: The data pipe 'R2eff - relax_disp (Fri Mar 15 > 14:03:20 2019)' already exists. > > Is there a way to rerun the analysis without reloading all of the input > files etc. as this is rather time-consuming. > The best is to save the relax state just after loading the data. Then just load the state in the GUI. Regards, Edward
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