1
Vote

missing output files with feature_selection_cv.py for UNIX

description

Hello;
I run feature_selection_cv.py for UNIX and I've got only the _mse.txt file. The other files, especially the most significant - _report.txt and _snps.cnv - are missing. The Log reports a wealth of warnings and a RunTime error ("invalid Display variable") at the end:

/usr/local/anaconda/lib/python2.7/site-packages/fastlmm/pyplink/plink.py:357: DeprecationWarning: using a non-integer number instead of an integer will result in an error in the future
byte_a = ba_raw.reshape((SP.ceil(0.25N),Sblock),order='F')
/usr/local/anaconda/lib/python2.7/site-packages/fastlmm/pyplink/plink.py:357: DeprecationWarning: using a non-integer number instead of an integer will result in an error in the future
byte_a = ba_raw.reshape((SP.ceil(0.25
N),Sblock),order='F')
Traceback (most recent call last):
File "/usr/local/anaconda/lib/python2.7/site-packages//fastlmm/feature_selection/feature_selection_cv.py", line 934, in <module>
result = main()
File "/usr/local/anaconda/lib/python2.7/site-packages//fastlmm/feature_selection/feature_selection_cv.py", line 926, in main
best_k, best_delta, best_obj, best_snps = fss.perform_selection(k_values, delta_values, args.strategy, output_prefix=args.output_prefix, select_by_ll=args.select_by_ll, runner=runner)
File "/usr/local/anaconda/lib/python2.7/site-packages//fastlmm/feature_selection/feature_selection_cv.py", line 440, in perform_selection
result = runner.run(perform_selection_distributable)
File "/usr/local/anaconda/lib/python2.7/site-packages/fastlmm/util/runner/Local.py", line 25, in run
result = run_all_in_memory(distributable)
File "/usr/local/anaconda/lib/python2.7/site-packages/fastlmm/util/runner/init.py", line 40, in run_all_in_memory
return work.reduce(result_sequence)
File "/usr/local/anaconda-2.0.1/lib/python2.7/site-packages/fastlmm/feature_selection/PerformSelectionDistributable.py", line 118, in reduce
best_k_mse, best_delta_mse, best_mse, best_delta_mse_interp, best_mse_interp = self.feature_selection_strategy.reduce_result(mse_cv, self.k_values, self.delta_values, self.strategy, self.output_prefix, best_delta_for_k, label="mse")
File "/usr/local/anaconda/lib/python2.7/site-packages//fastlmm/feature_selection/feature_selection_cv.py", line 520, in reduce_result
pylab.figure()
File "/usr/local/anaconda/lib/python2.7/site-packages/matplotlib/pyplot.py", line 423, in figure
**kwargs)
File "/usr/local/anaconda/lib/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py", line 31, in new_figure_manager
return new_figure_manager_given_figure(num, thisFig)
File "/usr/local/anaconda/lib/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py", line 38, in new_figure_manager_given_figure
canvas = FigureCanvasQTAgg(figure)
File "/usr/local/anaconda/lib/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py", line 70, in init
FigureCanvasQT.__init__( self, figure )
File "/usr/local/anaconda/lib/python2.7/site-packages/matplotlib/backends/backend_qt4.py", line 207, in init
_create_qApp()
File "/usr/local/anaconda/lib/python2.7/site-packages/matplotlib/backends/backend_qt4.py", line 62, in _create_qApp
raise RuntimeError('Invalid DISPLAY variable')

RuntimeError: Invalid DISPLAY variable

Could anyone tell what's going wrong ? Any clues that could help to fix the problem will be greatly appreciated.

PS: I installed the same program on my PC and it works perfectly so the problem is likely to come from a bad interaction between this program and the UNIX Platform that I use.

Thanks in advance for the hand.

P. Dubreuil

comments