bugrelax - Bugs: bug #20563, Relax failed while running final...

 
 
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bug #20563: Relax failed while running final execution (in the model-free auto-analysis in the GUI)

Submitted by:  Stanislava Panova <stacy>
Submitted on:  Tue 26 Feb 2013 05:32:16 PM UTC  
 
Category: relax's source codeSpecific analysis category: None
Priority: 5 - NormalSeverity: 5 - Blocker
Status: FixedAssigned to: Edward d Auvergne <bugman>
Originator Name: Open/Closed: Closed
Release: 2.2.2Operating System: All systems

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

Mon 11 Mar 2013 12:31:17 PM UTC, SVN revision 18764:

Merged revisions 18763 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r18763 | bugman | 2013-03-11 13:30:22 +0100 (Mon, 11 Mar 2013) | 6 lines

Created the Mf.test_bug_20563_missing_ri_error system test to catch bug #20563.

The bug report is at https://gna.org/bugs/?20563. The data added to the test suite is a highly
truncated data set of a analysis completed using the data attached to the bug report.
........

(Browse SVN revision 18764)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 11 Mar 2013 12:30:23 PM UTC, SVN revision 18763:

Created the Mf.test_bug_20563_missing_ri_error system test to catch bug #20563.

The bug report is at https://gna.org/bugs/?20563. The data added to the test suite is a highly
truncated data set of a analysis completed using the data attached to the bug report.

(Browse SVN revision 18763)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Sat 09 Mar 2013 10:46:57 AM UTC, SVN revision 18727:

Merged revisions 18726 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r18726 | bugman | 2013-03-09 11:38:38 +0100 (Sat, 09 Mar 2013) | 9 lines

Fix for bug #20563 (https://gna.org/bugs/?20563), the end failure of the model-free auto-analysis.

This was reported by Stanislava Panova (https://gna.org/users/stacy). The problem was related to
the Monte Carlo simulations. The generic_fns.monte_carlo.create_data() function is now asking for
the errors associated with a certain data point, even if that data point does not exist. The
solution was to check if the relaxation data ID string is present in spin.ri_data_err before
accessing the key-value pair (in the specific API _return_error_relax_data() common method).
........

(Browse SVN revision 18727)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Sat 09 Mar 2013 10:38:38 AM UTC, SVN revision 18726:

Fix for bug #20563 (https://gna.org/bugs/?20563), the end failure of the model-free auto-analysis.

This was reported by Stanislava Panova (https://gna.org/users/stacy). The problem was related to
the Monte Carlo simulations. The generic_fns.monte_carlo.create_data() function is now asking for
the errors associated with a certain data point, even if that data point does not exist. The
solution was to check if the relaxation data ID string is present in spin.ri_data_err before
accessing the key-value pair (in the specific API _return_error_relax_data() common method).

(Browse SVN revision 18726)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Sat 09 Mar 2013 08:34:30 AM UTC, comment #3:

This bug took a long time to reproduce. I've attached a script which cuts the time down significantly. Note the script is only good for catching the bug, it's model-free results are rubbish.

(file #17412)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Fri 08 Mar 2013 08:35:54 AM UTC, comment #2:

For more details, see the following threads (each link contains the same email thread):

http://thread.gmane.org/gmane.science.nmr.relax.devel/3776
http://marc.info/?l=relax-devel&m=136189994125191&w=2
http://www.mail-archive.com/relax-devel@gna.org/index.html#03707
https://mail.gna.org/public/relax-devel/2013-02/msg00051.html

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 26 Feb 2013 05:35:30 PM UTC, comment #1:

I was running model-free analysis.

Stanislava Panova <stacy>
Tue 26 Feb 2013 05:32:16 PM UTC, original submission:

Relax failed while running final execution after running local_tm and sphere mode successfully.

Exception raised in thread.

Traceback (most recent call last):
File "/usr/local/relax-2.2.2/gui/analyses/execute.py", line 87, in run
self.run_analysis()
File "/usr/local/relax-2.2.2/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 "/usr/local/relax-2.2.2/auto_analyses/dauvergne_protocol.py", line 234, in _init_
self.execute()
File "/usr/local/relax-2.2.2/auto_analyses/dauvergne_protocol.py", line 734, in execute
self.interpreter.monte_carlo.create_data()
File "/usr/local/relax-2.2.2/prompt/uf_objects.py", line 219, in _call_
self._backend(*new_args, **uf_kargs)
File "/usr/local/relax-2.2.2/generic_fns/monte_carlo.py", line 76, in create_data
error = return_error(data_index)
File "/usr/local/relax-2.2.2/specific_fns/api_common.py", line 260, in _return_error_relax_data
error.append(spin.ri_data_err[ri_id])
KeyError: '4'

PS I have tried to analyze relaxation data and it failed. 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
8)protocol sphere
9)execute relax
10)protocol final
11)execute relax

Stanislava Panova <stacy>

 

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Attached Files
file #17412:  dauvergne_protocol.py added by bugman (12kB - text/x-python - This script triggers the bug with the data attached by Stacy. Just change DIFF_MODEL to 'local_tm', then 'sphere', then 'final'.)
file #17348:  R2604 added by stacy (2kB - application/octet-stream)
file #17349:  R1850 added by stacy (2kB - application/octet-stream)
file #17350:  R2863 added by stacy (2kB - application/octet-stream)
file #17351:  NoeRelN added by stacy (2kB - application/octet-stream)

 

Depends on the following items: None found

Items that depend on this one: None found

 

Carbon-Copy List
  • -unavailable- added by bugman (Posted a comment)
  • -unavailable- added by stacy (Submitted the item)
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    Follow 12 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Sat 09 Mar 2013 10:47:15 AM UTCbugmanStatusConfirmed=>Fixed
      Open/ClosedOpen=>Closed
    Sat 09 Mar 2013 08:34:30 AM UTCbugmanAttached File-=>Added dauvergne_protocol.py, #17412
      CategoryGUI=>relax's source code
      StatusNone=>Confirmed
      Operating SystemGNU/Linux=>All systems
      SummaryRelax failed while running final execution=>Relax failed while running final execution (in the model-free auto-analysis in the GUI)
    Fri 08 Mar 2013 08:35:54 AM UTCbugmanAssigned toNone=>bugman
    Tue 26 Feb 2013 05:32:16 PM UTCstacyAttached File-=>Added R2604, #17348
      Attached File-=>Added R1850, #17349
      Attached File-=>Added R2863, #17350
      Attached File-=>Added NoeRelN, #17351
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