ModelSEED/Model-SEED-core — Issue #80: [Feature request] Misspeling Issue, FBA functions options
Author: Jose-Faria
Created: 2011-11-02 20:31:44+00:00
State: open

As you can see by the 3 examples bellow, due to misspell issues I am getting growth... the correct case is the 3rd one and as you guys can see no growth is observed.

Could a check for misspelling be implemented and return an error message?

[jplfaria@biologin-4 bin]$ ./fbacheckgrowth -model iJR904.24902 -media Carbon-D-Glucose -options thermo:themoerror
Creating the model file: /vol/model-dev/MODEL_DEV_DB/ReactionDB/MFAToolkitOutputFiles/2400782/iJR904.24902.tbl
Creating biochemistry provenance files
mkdir: cannot create directory `/vol/model-dev/MODEL_DEV_DB/ReactionDB/MFAToolkitOutputFiles/2400782/MFAOutput': File exists
iJR904.24902 grew in Carbon-D-Glucose media with rate:0.472273 gm biomass/gm CDW hr.

[jplfaria@biologin-4 bin]$ ./fbacheckgrowth -model iJR904.24902 -media Carbon-D-Glucose -options thermo:thermoerror
Creating the model file: /vol/model-dev/MODEL_DEV_DB/ReactionDB/MFAToolkitOutputFiles/2400792/iJR904.24902.tbl
Creating biochemistry provenance files
mkdir: cannot create directory `/vol/model-dev/MODEL_DEV_DB/ReactionDB/MFAToolkitOutputFiles/2400792/MFAOutput': File exists
iJR904.24902 grew in Carbon-D-Glucose media with rate:0.472273 gm biomass/gm CDW hr.

[jplfaria@biologin-4 bin]$ ./fbacheckgrowth -model iJR904.24902 -media Carbon-D-Glucose -options thermo;thermoerror
Creating the model file: /vol/model-dev/MODEL_DEV_DB/ReactionDB/MFAToolkitOutputFiles/2400802/iJR904.24902.tbl
Creating biochemistry provenance files
mkdir: cannot create directory `/vol/model-dev/MODEL_DEV_DB/ReactionDB/MFAToolkitOutputFiles/2400802/MFAOutput': File exists
IBM ILOG License Manager: "IBM ILOG Optimization Suite for Academic Initiative" is accessing CPLEX 12 with option(s): "e m b q ".
iJR904.24902 failed to grow in Carbon-D-Glucose media.
Biomass compounds cpd00119,cpd15654,cpd00062,cpd00345,cpd00107,cpd00357,cpd00129,cpd00051,cpd00023,cpd00264,cpd00356,cpd00041,cpd00052,cpd00039,cpd00026,cpd00118,cpd00053 could not be generated!