BioSystemsUM
Infeasible error in rFBA
Hello, I am encountering an issue while running the "rfba.optimize()" & "find_conflicts()" analysis using the provided guide and code. Despite following the instructions exactly, the solution consistently returns an objective value of 0, and the following error is raised:
--------------------------------< error >------------------------------------- RuntimeError Traceback (most recent call last) Cell In[21], line 2 1 # we can see that 3 regulators are affecting the following essential genes: b2574; b1092; b3730 ----> 2 repressed_genes, repressed_reactions = find_conflicts(model) 3 repressed_genes
File ~/insilico_data/JSY/rFBA/mewpy/src/mewpy/germ/analysis/integrated_analysis.py:475, in find_conflicts(model, strategy, constraints, initial_state) 472 solution = FBA(model).build().optimize(solver_kwargs={'constraints': constraints}) 474 if not solution.objective_value: --> 475 raise RuntimeError('FBA solution is not feasible (objective value is 0). To find inconsistencies, ' 476 'the metabolic model must be feasible.') 478 # 2. it performs an essential genes analysis using FBA 479 from mewpy.germ.analysis.metabolic_analysis import single_gene_deletion
RuntimeError: FBA solution is not feasible (objective value is 0). To find inconsistencies, the metabolic model must be feasible.
[ALL Script]
import sys import os import warnings import pandas as pd warnings.filterwarnings("ignore") current_dir = os.getcwd() subdirs = [os.path.join(current_dir, d) for d in os.listdir(current_dir) if os.path.isdir(os.path.join(current_dir, d))] for subdir in subdirs: sys.path.append(subdir)
from mewpy.io import Reader, Engines, read_model from mewpy.germ.analysis import find_conflicts from reframed.core import model
from cobra import * from cobra.io import load_matlab_model, load_json_model, read_sbml_model path = str(subdirs[0][:-10]) model_path = str(path) + '/examples/models/germ/iJR904.xml' tf_path = str(path) + '/examples/models/germ/iMC1010.csv'
cobra_model = read_met_model('iJR904.xml', str(path) + '/examples/models/germ/') changeBound(cobra_model, 'EX_glc_DASH_D_e', -100, -100) sol = cobra_model.optimize() sol ## biomass flux = 3.3
path = str(subdirs[0][:-10]) model_path = str(path) + '/examples/models/germ/iJR904.xml' tf_path = str(path) + '/examples/models/germ/iMC1010.csv' imc1010_gem_reader = Reader(Engines.MetabolicSBML, model_path) imc1010_trn_reader = Reader(Engines.BooleanRegulatoryCSV, tf_path, sep=',', id_col=0, rule_col=4, aliases_cols=[1, 2, 3], header=0) model = read_model(imc1010_gem_reader, imc1010_trn_reader) repressed_genes, repressed_reactions = find_conflicts(model) repressed_genes ## --> raise error (infeasible)
from mewpy.germ.analysis import RFBA initial_state = { 'Stringent': 0.0, 'high-NAD': 0.0, 'AGDC': 0.0, } rfba = RFBA(model).build() solution = rfba.optimize(initial_state=initial_state) solution ## sol is zero
from mewpy.germ.analysis import SRFBA srfba = SRFBA(model).build() solution = srfba.optimize() solution ## sol is zero, too...
