jubra / gemeditor Goto Github PK

python -m GEMEditor.run --file=../Models/iJB1325_HP.json 
objc[1476]: Class FIFinderSyncExtensionHost is implemented in both /System/Library/PrivateFrameworks/FinderKit.framework/Versions/A/FinderKit (0x7fffa923e3f0) and /System/Library/PrivateFrameworks/FileProvider.framework/OverrideBundles/FinderSyncCollaborationFileProviderOverride.bundle/Contents/MacOS/FinderSyncCollaborationFileProviderOverride (0x1325dc8f50). One of the two will be used. Which one is undefined.
Scaling...
 A: min|aij| =  1.000e+00  max|aij| =  1.000e+00  ratio =  1.000e+00
Problem data seem to be well scaled
Traceback (most recent call last):
  File "/Users/zuck016/Projects/AgileBio/A.niger/GEMEditor/GEMEditor/main/model/tabs.py", line 859, in run_analysis
    self.analyses[selected_analysis](selected_solver)
  File "/Users/zuck016/Projects/AgileBio/A.niger/GEMEditor/GEMEditor/main/model/tabs.py", line 872, in run_parsimonous
    solution = pfba(self.model)
  File "/Users/zuck016/.pyenv/versions/anaconda3-2020.11/envs/idp_new/lib/python3.6/site-packages/cobra/flux_analysis/parsimonious.py", line 99, in pfba
    fraction_of_optimum=fraction_of_optimum, reactions=reactions)
  File "/Users/zuck016/.pyenv/versions/anaconda3-2020.11/envs/idp_new/lib/python3.6/site-packages/cobra/flux_analysis/parsimonious.py", line 164, in _pfba_optlang
    fraction_of_optimum=fraction_of_optimum)
  File "/Users/zuck016/.pyenv/versions/anaconda3-2020.11/envs/idp_new/lib/python3.6/site-packages/cobra/flux_analysis/parsimonious.py", line 133, in add_pfba
    for variable in variables]), direction='min', sloppy=True,
  File "/Users/zuck016/.pyenv/versions/anaconda3-2020.11/envs/idp_new/lib/python3.6/site-packages/cobra/flux_analysis/parsimonious.py", line 133, in <listcomp>
    for variable in variables]), direction='min', sloppy=True,
AttributeError: module 'sympy' has no attribute 'singleton'
Abort trap: 6
bash-3.2$