Hi, I have a problem finding biomass when I simulate the model built with modelseed using smetana, have you tried how the modelseed model should be modified?
(py38) C:\Users\wupen>python C:\Users\wupen\Program\Anaconda3\envs\py38\Scripts\smetana D:\jupyternotebook\Y_YL_model\ac_final_WP1376_03.xml D:\jupyternotebook\Y_YL_model\st_process_atp_compart.xml -v -d --molweight --zeros --flavor cobra
Loading community: all
Traceback (most recent call last):
File "C:\Users\wupen\Program\Anaconda3\envs\py38\Scripts\smetana", line 89, in
main(
File "C:\Users\wupen\Program\Anaconda3\envs\py38\lib\site-packages\smetana\interface.py", line 338, in main
medium_id, env = define_environment(medium, media_db, community, mode, verbose, min_mol_weight, use_lp)
File "C:\Users\wupen\Program\Anaconda3\envs\py38\lib\site-packages\smetana\interface.py", line 118, in define_environment
env = minimal_environment(community, verbose=verbose, min_mol_weight=min_mol_weight, use_lp=use_lp,
File "C:\Users\wupen\Program\Anaconda3\envs\py38\lib\site-packages\smetana\smetana.py", line 373, in minimal_environment
exch_reactions = set(community.merged.get_exchange_reactions())
File "C:\Users\wupen\Program\Anaconda3\envs\py38\lib\site-packages\smetana\legacy.py", line 203, in merged
self._merged_model = self.generate_merged_model()
File "C:\Users\wupen\Program\Anaconda3\envs\py38\lib\site-packages\smetana\legacy.py", line 271, in generate_merged_model
models_missing_biomass = [m.id for m in self._organisms.values() if not m.biomass_reaction]
File "C:\Users\wupen\Program\Anaconda3\envs\py38\lib\site-packages\smetana\legacy.py", line 271, in
models_missing_biomass = [m.id for m in self._organisms.values() if not m.biomass_reaction]
File "C:\Users\wupen\Program\Anaconda3\envs\py38\lib\site-packages\reframed\core\cbmodel.py", line 190, in biomass_reaction
self._detect_biomass_reaction()
File "C:\Users\wupen\Program\Anaconda3\envs\py38\lib\site-packages\reframed\core\cbmodel.py", line 213, in _detect_biomass_reaction
raise RuntimeError(f"No biomass reaction identified from model objective.")
RuntimeError: No biomass reaction identified from model objective.
Hi, I have a problem finding biomass when I simulate the model built with modelseed using smetana, have you tried how the modelseed model should be modified?
(py38) C:\Users\wupen>python C:\Users\wupen\Program\Anaconda3\envs\py38\Scripts\smetana D:\jupyternotebook\Y_YL_model\ac_final_WP1376_03.xml D:\jupyternotebook\Y_YL_model\st_process_atp_compart.xml -v -d --molweight --zeros --flavor cobra Loading community: all Traceback (most recent call last): File "C:\Users\wupen\Program\Anaconda3\envs\py38\Scripts\smetana", line 89, in
main(
File "C:\Users\wupen\Program\Anaconda3\envs\py38\lib\site-packages\smetana\interface.py", line 338, in main
medium_id, env = define_environment(medium, media_db, community, mode, verbose, min_mol_weight, use_lp)
File "C:\Users\wupen\Program\Anaconda3\envs\py38\lib\site-packages\smetana\interface.py", line 118, in define_environment
env = minimal_environment(community, verbose=verbose, min_mol_weight=min_mol_weight, use_lp=use_lp,
File "C:\Users\wupen\Program\Anaconda3\envs\py38\lib\site-packages\smetana\smetana.py", line 373, in minimal_environment
exch_reactions = set(community.merged.get_exchange_reactions())
File "C:\Users\wupen\Program\Anaconda3\envs\py38\lib\site-packages\smetana\legacy.py", line 203, in merged
self._merged_model = self.generate_merged_model()
File "C:\Users\wupen\Program\Anaconda3\envs\py38\lib\site-packages\smetana\legacy.py", line 271, in generate_merged_model
models_missing_biomass = [m.id for m in self._organisms.values() if not m.biomass_reaction]
File "C:\Users\wupen\Program\Anaconda3\envs\py38\lib\site-packages\smetana\legacy.py", line 271, in
models_missing_biomass = [m.id for m in self._organisms.values() if not m.biomass_reaction]
File "C:\Users\wupen\Program\Anaconda3\envs\py38\lib\site-packages\reframed\core\cbmodel.py", line 190, in biomass_reaction
self._detect_biomass_reaction()
File "C:\Users\wupen\Program\Anaconda3\envs\py38\lib\site-packages\reframed\core\cbmodel.py", line 213, in _detect_biomass_reaction
raise RuntimeError(f"No biomass reaction identified from model objective.")
RuntimeError: No biomass reaction identified from model objective.