bugrelax - Bugs: bug #20464, GUI model-free analysis failed in...

 
 
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bug #20464: GUI model-free analysis failed in _minimise_data_setup() with "KeyError: 'R2_600'".

Submitted by:  None
Submitted on:  Wed 30 Jan 2013 05:23:58 PM UTC  
 
Category: relax's source codeSeverity: 5 - Blocker
Priority: 5 - NormalStatus: Fixed
Privacy: PublicAssigned to: Edward d Auvergne <bugman>
Originator Name: Stanislava PanovaOriginator Email: -unavailable-
Open/Closed: ClosedRelease: 2.1.2
Operating System: All systems

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(Jump to the original submission Jump to the original submission)

Fri 01 Feb 2013 10:31:41 AM UTC, comment #8:

For more details, see the thread at http://thread.gmane.org/gmane.science.nmr.relax.devel/3707.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Fri 01 Feb 2013 10:22:51 AM UTC, SVN revision 18330:

Merged revisions 18328-18329 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r18328 | bugman | 2013-02-01 11:19:09 +0100 (Fri, 01 Feb 2013) | 6 lines

Created the Mf.test_bug_20464_missing_ri_data system test to catch bug #20464.

The data comes from the bug report submitted by Stanislava Panova (stpanova att gmail dot com) at
https://gna.org/bugs/?20464.
........
r18329 | bugman | 2013-02-01 11:22:16 +0100 (Fri, 01 Feb 2013) | 7 lines

Fix for bug #20464 (https://gna.org/bugs/?20464).

The problem was the previously missing data had a value of None whereas now the dictionary element
can be missing. Checks have been added to make sure the spin specific relaxation data structures
have the key corresponding to the data.
........

(Browse SVN revision 18330)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Fri 01 Feb 2013 10:22:16 AM UTC, SVN revision 18329:

Fix for bug #20464 (https://gna.org/bugs/?20464).

The problem was the previously missing data had a value of None whereas now the dictionary element
can be missing. Checks have been added to make sure the spin specific relaxation data structures
have the key corresponding to the data.

(Browse SVN revision 18329)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Fri 01 Feb 2013 10:19:09 AM UTC, SVN revision 18328:

Created the Mf.test_bug_20464_missing_ri_data system test to catch bug #20464.

The data comes from the bug report submitted by Stanislava Panova (stpanova att gmail dot com) at
https://gna.org/bugs/?20464.

(Browse SVN revision 18328)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 31 Jan 2013 11:56:26 AM UTC, comment #4:

I have tried to deselect residues 10 and 36 deselected and it is still not working:

Exception raised in thread.

Traceback (most recent call last):
File "gui/analyses/execute.pyc", line 87, in run
File "gui/analyses/auto_model_free.pyc", line 808, in run_analysis
File "auto_analyses/dauvergne_protocol.pyc", line 234, in _init_
File "auto_analyses/dauvergne_protocol.pyc", line 558, in execute
File "auto_analyses/dauvergne_protocol.pyc", line 816, in multi_model
File "prompt/uf_objects.pyc", line 219, in _call_
File "generic_fns/results.pyc", line 131, in write
File "relax_io.pyc", line 526, in open_write_file
RelaxError: RelaxError: Cannot open the file '/Volumes/relax/relax.app/Contents/Resources/local_tm/tm0/results.bz2'. No such file or directory.

Stanislava Panova <stacy>
Thu 31 Jan 2013 11:20:25 AM UTC, comment #3:

Sorry, I am quite ignorant about fixing bugs. Should I add the patch file somewhere or just solve the problem by deselecting residue? Thanks in advance.

Stanislava Panova <stacy>
Thu 31 Jan 2013 09:57:11 AM UTC, comment #2:

A temporary fix for this issue is to deselect residue 36, as this has only 3 data points compared to all others with 4. This problem is a real bug in relax and a fix is being worked on. I have followed all your steps and saved a relax state file prior to executing relax. I have removed all residues except 10 and 36, and can now trigger this bug using the relax scripting mode with a simple script (modified from sample_scripts/model_free/dauvergne_protocol.py). I will add the relax state file and script to the relax test suite to be sure that this bug never returns! These files are attached.

(file #17065, file #17066)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 31 Jan 2013 09:18:04 AM UTC, comment #1:

The true error message is:

Exception raised in thread.

Traceback (most recent call last):
File "gui/analyses/execute.py", line 87, in run
self.run_analysis()
File "gui/analyses/auto_model_free.py", line 808, in run_analysis
dauvergne_protocol.dAuvergne_protocol(pipe_name=self.data.pipe_name, pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir, diff_model=self.data.global_models, mf_models=self.data.mf_models, local_tm_models=self.data.local_tm_models, grid_inc=self.data.inc, diff_tensor_grid_inc=self.data.diff_tensor_grid_inc, mc_sim_num=self.data.mc_sim_num, max_iter=self.data.max_iter, conv_loop=self.data.conv_loop)
File "auto_analyses/dauvergne_protocol.py", line 234, in _init_
self.execute()
File "auto_analyses/dauvergne_protocol.py", line 558, in execute
self.multi_model(local_tm=True)
File "auto_analyses/dauvergne_protocol.py", line 808, in multi_model
self.interpreter.grid_search(inc=self.grid_inc)
File "prompt/uf_objects.py", line 219, in _call_
self._backend(new_args, *uf_kargs)
File "generic_fns/minimise.py", line 140, in grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints, verbosity=verbosity)
File "specific_fns/model_free/mf_minimise.py", line 1498, in grid_search
self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc, constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File "specific_fns/model_free/mf_minimise.py", line 1769, in minimise
self._minimise_data_setup(data_store, min_algor, num_data_sets, opt_params.min_options, spin=spin, sim_index=sim_index)
File "specific_fns/model_free/mf_minimise.py", line 1087, in _minimise_data_setup
err = spin.ri_data_err[ri_id]
KeyError: 'R2_600'

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Wed 30 Jan 2013 05:23:58 PM UTC, original submission:

I have tried calculate rotational correlation time and I failed. First of all to describe main steps:
1)load sequence from NOE data file
2)check spin.name, spin.element, spin.isotope
3)load relaxation data: 4 files (R1, R2, NOE for 800 MHz and R2 for 600MHz)
3)sequence.attach_protons()
4)dipolar relaxation (as I don't have pdb file, I have skipped first part and applyed only magnetic dipolar relaxation setup)
5)csa relaxation
6)protocol model local tm
7) execute relax

It is giving me
Exception raised in thread.

Traceback (most recent call last):
File "gui/analyses/execute.pyc", line 87, in run
File "gui/analyses/auto_model_free.pyc", line 808, in run_analysis
File "auto_analyses/dauvergne_protocol.pyc", line 234, in _init_
File "auto_analyses/dauvergne_protocol.pyc", line 558, in execute
File "auto_analyses/dauvergne_protocol.pyc", line 808, in multi_model
File "prompt/uf_objects.pyc", line 219, in _call_
File "generic_fns/minimise.pyc", line 140, in grid_search
File "specific_fns/model_free/mf_minimise.pyc", line 1498, in grid_search
File "specific_fns/model_free/mf_minimise.pyc", line 1769, in minimise
File "specific_fns/model_free/mf_minimise.pyc", line 1087, in _minimise_data_setup
KeyError: 'R2_600'

Thanks in advance,
Stacy

Anonymous

 

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Attach File(s):
   
   
Comment:
   

Attached Files
file #17067:  patch added by bugman (876B - application/octet-stream - A possible fix for this bug. This is a standard patch file.)
file #17065:  state.bz2 added by bugman (2kB - application/x-bzip - The saved relax state with all residues but 10 and 36 removed and the relax script which triggers the bug. These will be added to the relax test suite.)
file #17066:  test.py added by bugman (1kB - application/octet-stream - The saved relax state with all residues but 10 and 36 removed and the relax script which triggers the bug. These will be added to the relax test suite.)
file #17053:  NoeRelN added by None (2kB - application/octet-stream - NOE, R1_800, R2_600, R2_800)
file #17054:  R2604 added by None (2kB - application/octet-stream - NOE, R1_800, R2_600, R2_800)
file #17055:  R1850 added by None (2kB - application/octet-stream - NOE, R1_800, R2_600, R2_800)
file #17056:  R2863 added by None (2kB - application/octet-stream - NOE, R1_800, R2_600, R2_800)

 

Depends on the following items: None found

Items that depend on this one: None found

 

Carbon-Copy List
  • -unavailable- added by stacy (Posted a comment)
  • -unavailable- added by bugman (Posted a comment)
  • -unavailable- added by None (Submitted the item)

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    Follow 15 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Fri 01 Feb 2013 10:29:59 AM UTCbugmanStatusIn Progress=>Fixed
      Open/ClosedOpen=>Closed
    Thu 31 Jan 2013 09:58:54 AM UTCbugmanAttached File-=>Added patch, #17067
    Thu 31 Jan 2013 09:57:11 AM UTCbugmanAttached File-=>Added state.bz2, #17065
      Attached File-=>Added test.py, #17066
      StatusConfirmed=>In Progress
    Thu 31 Jan 2013 09:18:03 AM UTCbugmanCategoryNone=>relax's source code
      StatusNone=>Confirmed
      Assigned toNone=>bugman
      Operating SystemMac OS X (Intel)=>All systems
      Summarymodel-free failed=>GUI model-free analysis failed in _minimise_data_setup() with "KeyError: 'R2_600'".
    Wed 30 Jan 2013 05:23:59 PM UTCNoneAttached File-=>Added NoeRelN, #17053
      Attached File-=>Added R2604, #17054
      Attached File-=>Added R1850, #17055
      Attached File-=>Added R2863, #17056
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