FVA gives back odd results

Patrickens commented 1 year ago

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 ```

Midnighter commented 1 year ago

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

Patrickens commented 1 year ago

Oich, my bad. Thank you! Ill close.

opencobra / cobrapy