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MATLAB is selecting SOFTWARE OPENGL rendering. < M A T L A B (R) > Copyright 1984-2020 The MathWorks, Inc. R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) November 23, 2020 To get started, type doc. For product information, visit www.mathworks.com. _____ _____ _____ _____ _____ | / ___| / _ \ | _ \ | _ \ / ___ \ | COnstraint-Based Reconstruction and Analysis | | | | | | | |_| | | |_| | | |___| | | The COBRA Toolbox - 2021 | | | | | | | _ { | _ / | ___ | | | |___ | |_| | | |_| | | | \ \ | | | | | Documentation: \_____| \_____/ |_____/ |_| \_\ |_| |_| | http://opencobra.github.io/cobratoolbox | > Checking if git is installed ... Done (version: 2.25.1). > Checking if the repository is tracked using git ... Done. > Checking if curl is installed ... Done. > Checking if remote can be reached ... Done. > Initializing and updating submodules (this may take a while)... Done. > Adding all the files of The COBRA Toolbox ... Done. > Define CB map output... set to svg. > TranslateSBML is installed and working properly. > Configuring solver environment variables ... - [----] ILOG_CPLEX_PATH: --> set this path manually after installing the solver ( see https://opencobra.github.io/cobratoolbox/docs/solvers.html ) - [----] GUROBI_PATH: --> set this path manually after installing the solver ( see https://opencobra.github.io/cobratoolbox/docs/solvers.html ) - [----] TOMLAB_PATH: --> set this path manually after installing the solver ( see https://opencobra.github.io/cobratoolbox/docs/solvers.html ) - [----] MOSEK_PATH: --> set this path manually after installing the solver ( see https://opencobra.github.io/cobratoolbox/docs/solvers.html ) Done. > Checking available solvers and solver interfaces ... Done. > Setting default solvers ... Done. > Saving the MATLAB path ... Done. - The MATLAB path was saved as ~/pathdef.m. > Summary of available solvers and solver interfaces Support LP MILP QP MIQP NLP ---------------------------------------------------------------------- gurobi active 1 1 1 1 - ibm_cplex active 0 0 0 0 - tomlab_cplex active 0 0 0 0 - glpk active 1 1 - - - mosek active 0 - 0 - - matlab active 0 - - - 0 pdco active 1 - 1 - - quadMinos active 0 - - - - dqqMinos active 0 - 0 - - cplex_direct active 0 0 0 - - cplexlp active 0 - - - - qpng passive - - 1 - - tomlab_snopt passive - - - - 0 lp_solve legacy 1 - - - - ---------------------------------------------------------------------- Total - 4 2 3 1 0 + Legend: - = not applicable, 0 = solver not compatible or not installed, 1 = solver installed. > You can solve LP problems using: 'gurobi' - 'glpk' - 'pdco' > You can solve MILP problems using: 'gurobi' - 'glpk' > You can solve QP problems using: 'gurobi' - 'pdco' > You can solve MIQP problems using: 'gurobi' > You can solve NLP problems using: > Checking for available updates ... > There are 7848 new commit(s) on <master> and 0 new commit(s) on <develop> [800dcf @ master] > You can update The COBRA Toolbox by running updateCobraToolbox() (from within MATLAB). Converting COBRA structure to RAVEN.. *************************************************************** GECKO: Adding enzyme constraints to a genome-scale model *************************************************************** Getting genome-scale model ready... Done! ================== Generating ecModel: ================== Retrieving EC numbers............................................ Done! Matching kcats............................................ Done! Adding enzymes to reactions............................................................... Done! Improving model with curated data....................................................................................... Done! Removing repeated rxn: r_0226No2 & r_0226No3 Removing repeated rxn: r_0438No1 & r_0438No2 Removing repeated rxn: r_0438No1 & r_0438No3 Removing repeated rxn: r_0438No1 & r_0438No4 Removing repeated rxn: r_0438No2 & r_0438No3 Removing repeated rxn: r_0438No2 & r_0438No4 Removing repeated rxn: r_0438No3 & r_0438No4 Removing repeated rxn: r_0439No1 & r_0439No2 Merging reactions: arm_r_0439 & r_0439No1 Merging reactions: arm_r_0543 & r_0543No1 Merging reactions: arm_r_1838 & r_1838No1 Removing unused protein: P00424 Removing unused protein: P18496 Removing unused protein: P22135 Removing unused protein: P32453 Removing unused protein: Q3E7B6 Removing incorrect pathways... Done! ============================================================== Generating ecModel with shared pool assumption (ecModel_batch): ============================================================== Calculating total abundance.................................................................... Done! WARNING: Reaction r_1663 is not present in the reaction list WARNING: Reaction r_4062 is not present in the reaction list WARNING: Reaction r_4064 is not present in the reaction list Matching data to enzymes in model... Done! Estimating GAM.............................................................. Done! Fitted GAM = 27.4 -> Error = 0.1816 [Warning: MATLAB has disabled some advanced graphics rendering features by switching to software OpenGL. For more information, click <a href="matlab:opengl('problems')">here</a>.] Total protein amount measured = 0 g/gDW Total enzymes measured = 0 enzymes Enzymes in model with 0 g/gDW = 0 enzymes Total protein amount not measured = 0.5 g/gDW Total enzymes not measured = 968 enzymes Total protein in model = 0.5 g/gDW The ECmodel is overconstrained! ******************* Limiting Kcats curation ******************* *Iteration #1 Automatic search // EC#: 5.4.99.7 Protein:P38604 Rxn#:3751 name: lanosterol synthase (No1) prev_Kcat:0.0019367 new_Kcat:4.0763 CC:0.63672 Err:-61.0431% *Iteration #2 Automatic search // EC#: 6.3.5.3 Protein:P38972 Rxn#:2991 name: 5'-phosphoribosylformyl glycinamidine synthetase (No1) prev_Kcat:0.05 new_Kcat:5.0675 CC:0.36184 Err:-47.1166% *Iteration #3 Automatic search // EC#: 4.2.1.20 Protein:P00931 Rxn#:4155 name: tryptophan synthase (indoleglycerol phosphate) (No1) prev_Kcat:0.022301 new_Kcat:775.75 CC:0.41185 Err:-25.3069% *Iteration #4 Automatic search // EC#: 6.3.4.- 6.3.4.9 6.3.4.10 6.3.4.11 6.3.4.15 Protein:P48445 Rxn#:3031 name: acetyl-CoA carboxylase, reaction (No1) prev_Kcat:1.23 new_Kcat:450000 CC:0.059866 Err:-20.8306% *Iteration #5 Automatic search // EC#: 2.1.1.14 Protein:P05694 Rxn#:3781 name: methionine synthase (No1) prev_Kcat:0.33 new_Kcat:3.5 CC:0.046422 Err:-17.513% *Iteration #6 Automatic search // EC#: 2.7.6.1 Protein:P32895 Rxn#:3984 name: phosphoribosylpyrophosphate synthetase (No1) prev_Kcat:0.65999 new_Kcat:1170 CC:0.044464 Err:-13.8436% *Iteration #7 Automatic search // EC#: 4.1.1.65 Protein:P39006 Rxn#:4659 name: PS decarboxylase (1-16:1, 2-16:1), mitochondrial membrane (No1) prev_Kcat:0.053334 new_Kcat:366.6667 CC:0.041758 Err:-10.2424% *Iteration #8 Automatic search // EC#: 1.1.1.302 Protein:P33312 Rxn#:2909 name: 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase (NADPH) (No1) prev_Kcat:0.00066666 new_Kcat:0.00066667 CC:0.042829 Err:-10.2424% *Iteration #9 Automatic search // EC#: 2.3.1.15 2.3.1.42 Protein:P36148 Rxn#:4383 name: glycerol-3-phosphate acyltransferase (16:1), ER membrane (No2) prev_Kcat:0.0918 new_Kcat:9.9733 CC:0.038586 Err:-6.8086% *************************************************************** Fitting sigma factor....................... Done! Saving simulation results files... File successfully saved. Sigma factor (fitted for growth on glucose): 0.49 ============= Saving models: ============= Saving ecYeastGEMv8.4.2: Converting RAVEN structure to COBRA.. Each model.subSystems{x} is a character array, and this format is retained. Document written Each model.subSystems{x} is a character array, and this format is retained. Saving ecYeastGEM_batchv8.4.2: Converting RAVEN structure to COBRA.. Each model.subSystems{x} is a character array, and this format is retained. Document written Each model.subSystems{x} is a character array, and this format is retained.
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