FVA gives back odd results
Patrickens opened this issue · 2 comments
Problem description
A dependency that Im using is trying to use cobra.flux_analysis.flux_variability_analysis and fails because there is a bug. The example below is with the e_coli_core model and Im using the gurobipy solver. When printing the reactions and bounds, and checking the bounds on the optlang.Variable objects, everything is as defined in the e_coli_core model, but this somehow still hangs.
Code Sample
from cobra.io import read_sbml_model
from cobra.flux_analysis import flux_variability_analysis
file = 'e_coli_core.xml'
model = read_sbml_model(file)
model.reactions.get_by_id('EX_glc__D_e').bounds = (-10.0, 0.0)
fva = flux_variability_analysis(model=model, processes=1)
As we can see in the output below, it seems that most minima are equal to the maxima, which is a bug. I have the feeling this is an optlang + gurobi backend issue. I don't use optlang much, so I wouldn't know how to address this.
FVA OUTPUT:
| minimum | maximum | |
|---|---|---|
| PFK | 7.477382 | 7.477382 |
| PFL | 0 | 0 |
| PGI | 4.860861 | 4.860861 |
| PGK | -16.0235 | -16.0235 |
| PGL | 4.959985 | 4.959985 |
| ACALD | 0 | 0 |
| AKGt2r | 0 | 0 |
| PGM | -14.7161 | -14.7161 |
| PIt2r | 3.214895 | 3.214895 |
| ALCD2x | 0 | 0 |
| ACALDt | 0 | 0 |
| ACKr | 0 | 0 |
| PPC | 2.504309 | 2.504309 |
| ACONTa | 6.00725 | 6.00725 |
| ACONTb | 6.00725 | 6.00725 |
| ATPM | 8.39 | 8.39 |
| PPCK | 0 | 0 |
| ACt2r | 0 | 0 |
| PPS | 0 | 0 |
| ADK1 | 0 | 0 |
| AKGDH | 5.064376 | 5.064376 |
| ATPS4r | 45.51401 | 45.51401 |
| PTAr | 0 | 0 |
| PYK | 1.758177 | 1.758177 |
| BIOMASS_Ecoli_core_w_GAM | 0.873922 | 0.873922 |
| PYRt2 | 0 | 0 |
| CO2t | -22.8098 | -22.8098 |
| RPE | 2.678482 | 2.678482 |
| CS | 6.00725 | 6.00725 |
| RPI | -2.2815 | -2.2815 |
| SUCCt2_2 | 0 | 0 |
| CYTBD | 43.59899 | 43.59899 |
| D_LACt2 | 0 | 0 |
| ENO | 14.71614 | 14.71614 |
| SUCCt3 | 0 | 0 |
| ETOHt2r | 0 | 0 |
| SUCDi | 5.064376 | 1000 |
| SUCOAS | -5.06438 | -5.06438 |
| TALA | 1.496984 | 1.496984 |
| THD2 | 0 | 0 |
| TKT1 | 1.496984 | 1.496984 |
| TKT2 | 1.181498 | 1.181498 |
| TPI | 7.477382 | 7.477382 |
| EX_ac_e | 0 | 0 |
| EX_acald_e | 0 | 0 |
| EX_akg_e | 0 | 0 |
| EX_co2_e | 22.80983 | 22.80983 |
| EX_etoh_e | 0 | 0 |
| EX_for_e | 0 | 0 |
| EX_fru_e | 0 | 0 |
| EX_fum_e | 0 | 0 |
| EX_glc__D_e | -10 | -10 |
| EX_gln__L_e | 0 | 0 |
| EX_glu__L_e | 0 | 0 |
| EX_h_e | 17.53087 | 17.53087 |
| EX_h2o_e | 29.17583 | 29.17583 |
| EX_lac__D_e | 0 | 0 |
| EX_mal__L_e | 0 | 0 |
| EX_nh4_e | -4.76532 | -4.76532 |
| EX_o2_e | -21.7995 | -21.7995 |
| EX_pi_e | -3.2149 | -3.2149 |
| EX_pyr_e | 0 | 0 |
| EX_succ_e | 0 | 0 |
| FBA | 7.477382 | 7.477382 |
| FBP | 0 | 0 |
| FORt2 | 0 | 0 |
| FORt | 0 | 0 |
| FRD7 | 0 | 994.9356 |
| FRUpts2 | 0 | 0 |
| FUM | 5.064376 | 5.064376 |
| FUMt2_2 | 0 | 0 |
| G6PDH2r | 4.959985 | 4.959985 |
| GAPD | 16.02353 | 16.02353 |
| GLCpts | 10 | 10 |
| GLNS | 0.223462 | 0.223462 |
| GLNabc | 0 | 0 |
| GLUDy | -4.54186 | -4.54186 |
| GLUN | 0 | 0 |
| GLUSy | 0 | 0 |
| GLUt2r | 0 | 0 |
| GND | 4.959985 | 4.959985 |
| H2Ot | -29.1758 | -29.1758 |
| ICDHyr | 6.00725 | 6.00725 |
| ICL | 0 | 0 |
| LDH_D | 0 | 0 |
| MALS | 0 | 0 |
| MALt2_2 | 0 | 0 |
| MDH | 5.064376 | 5.064376 |
| ME1 | 0 | 0 |
| ME2 | 0 | 0 |
| NADH16 | 38.53461 | 38.53461 |
| NADTRHD | 0 | 0 |
| NH4t | 4.765319 | 4.765319 |
| O2t | 21.79949 | 21.79949 |
| PDH | 9.282533 | 9.282533 |
Context
python -c "import cobra;cobra.show_versions()"
-->
System Information
==================
OS Windows
OS-release 10
Python 3.8.13
Package Versions
================
appdirs 1.4.4
black ; extra == 'development' not installed
bumpversion ; extra == 'development' not installed
cobra 0.26.2
depinfo 1.7.0
diskcache 5.4.0
future 0.18.2
httpx 0.23.0
importlib-resources 5.9.0
isort ; extra == 'development' not installed
numpy 1.23.3
optlang 1.6.1
pandas 1.4.4
pip 22.2.2
poetry 1.4.1
pydantic 1.10.2
python-libsbml 5.19.6
rich 12.5.1
ruamel.yaml 0.17.21
scipy 1.9.1
setuptools 67.6.0
swiglpk 5.0.8
tox ; extra == 'development' not installed
wheel 0.37.1
You need to allow for a little bit of variability by choosing a fraction of the optimum https://cobrapy.readthedocs.io/en/latest/simulating.html#Running-FVA
Oich, my bad. Thank you! Ill close.