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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: 'glpk' - 'pdco' > You can solve MILP problems using: 'glpk' > You can solve QP problems using: 'pdco' > You can solve MIQP problems using: > You can solve NLP problems using: > Checking for available updates ... > There are 8010 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...
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