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GonghuaLi / GPMM

Genome-wide precision metabolic modeling
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When running run_GPMM, an error occur. #2

Open yiranzhimo opened 2 years ago

yiranzhimo commented 2 years ago

Hello, Thank you for your guys' work. But when I running GPMM, something puzzling happened.

  1. I have installed Matlab, Cobra toolbox and FastMM;
  2. I downloaded GPMM package, and enter the dictionary in matlab, but when I running the command: run_GPMM,an error occur:

Output argument "varargout{11}" (and possibly others) not assigned a value in the execution with "getCobraSolverParams" function. 出错 parseSolverParameters (第 43 行) [solverVars{:}] = getCobraSolverParams(problemType,cobraSolverParameters,struct('solver',defaultSolver)); 出错 solveCobraLP (第 123 行) [cobraParams, solverParams] = parseSolverParameters('LP',varargin{:}); 出错 optimizeCbModel (第 204 行) solution = solveCobraLP(LPproblem); 出错 gimme_by_reaction>solveGimme (第 307 行) FBAsolution = optimizeCbModel(modelIrrev); 出错 gimme_by_reaction (第 230 行) [reactionActivity,reactionActivityIrrev,model2gimme,gimmeSolution] = solveGimme(model,options,expressionCol,cutoff); 出错 Reduce_recon3 (第 48 行) [tissueModel,Rxns] = gimme_by_reaction(outmodel, ExpressedRxns,UnExpressedRxns,[],[idATP,0.9]);

截图 2022-09-09 09-23-51

GonghuaLi commented 2 years ago

Thank you for your interesting in GPMM.

  1. Please use our pre-compiled version of cobra:https://github.com/GonghuaLi/extern_tools/blob/main/cobratoolbox-3.0.4_precompiled.rar.

  2. Please install cplex solver and add cplex to matlab path

  3. In FastMM directory: Install FastMM in matlab and run "Insatall", add FastMM to the matlab path, add the . /bin file into env-Path, export PATH="~~your fastamm path/bin:$PATH"

  4. If you are running in linux, set following env: export PATH="your matlab path/R20??/bin:$PATH" export PATH="your cplex path/Cplex/cplex/bin/x86-64_linux:$PATH" export PATH="your matlab path/R20??/bin/glnxa64:$PATH" export PATH="your FastMM path/bin:$PATH"

  5. Test in GPMM directory: load('./data/Recon3_v1.mat') changeCobraSolver('cplex') fluxes = FastMM_FVA(Recon3) optimizeCbModel(Recon3)

---Hope these suggestion can solve your issue.

Gong-Hua Li