Closed automator-metatlas closed 3 years ago
MATLAB is selecting SOFTWARE OPENGL rendering. _____ _____ _____ _____ _____ | / ___| / _ \ | _ \ | _ \ / ___ \ | 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_1341 & r_1342 Removing repeated rxn: r_1349 & r_1350 Removing repeated rxn: r_1360 & r_1361 Removing repeated rxn: r_1362 & r_1457 Removing repeated rxn: r_1372 & r_1373 Removing repeated rxn: r_1383 & r_1384 Removing repeated rxn: r_1522 & r_1523 Removing repeated rxn: r_1524 & r_1525 Removing repeated rxn: r_1535 & r_1536_REV Removing repeated rxn: r_1538 & r_1539 Removing repeated rxn: r_1543 & r_1542_REV Removing repeated rxn: r_1545 & r_1546 Removing repeated rxn: r_1555 & r_1553_REV Removing repeated rxn: r_1578 & r_1579 Removing repeated rxn: r_1582 & r_1583 Removing repeated rxn: r_1591 & r_1592 Removing repeated rxn: r_1593 & r_1594_REV Removing repeated rxn: r_1594 & r_1595 Removing repeated rxn: r_1602 & r_1603 Removing repeated rxn: r_1609 & r_1607_REV Removing repeated rxn: r_1620 & r_1619_REV Removing repeated rxn: r_1628 & r_1629 Removing repeated rxn: r_1640 & r_1641 Removing repeated rxn: r_1647 & r_1648 Removing repeated rxn: r_1649 & r_1650 Removing repeated rxn: r_1654 & r_1655 Removing repeated rxn: r_1670 & r_1669_REV Removing repeated rxn: r_1672 & r_1674_REV Removing repeated rxn: r_1674 & r_1675 Removing repeated rxn: r_1682 & r_1683_REV Removing repeated rxn: r_1683 & r_1684 Removing repeated rxn: r_1690 & r_1691_REV Removing repeated rxn: r_1691 & r_1692 Removing repeated rxn: r_1713 & r_1714_REV Removing repeated rxn: r_1714 & r_1715 Removing repeated rxn: r_1716 & r_1717_REV Removing repeated rxn: r_1717 & r_1718 ============================================================== Generating ecModel with shared pool assumption (ecModel_batch): ============================================================== prot_abundance file is empty or not available. A default value of f=0.5 is set instead WARNING: Reaction r_1771 is not present in the reaction list Matching data to enzymes in model... Done! Estimating GAM.............................................................. Done! Fitted GAM = 53.4 -> Error = 0.31657 [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 = 0.546 g/gDW Total enzymes not measured = 716 enzymes Total protein in model = 0.546 g/gDW The ECmodel is overconstrained! ******************* Limiting Kcats curation ******************* *Iteration #1 Automatic search // EC#: 1.14.19.41 Protein:W0TF60 Rxn#:1934 name: 5,7,24(28)-ergostatrienol[r]+NADP(+)[r]=>ergosta-5,7,22,24(28)-tetraen-3beta-ol[r]+H+[r]+NADPH[r] (No1) prev_Kcat:0.015 new_Kcat:0.17 CC:0.39894 Err:-20.0879% *Iteration #2 Automatic search // EC#: 6.3.5.3 Protein:W0TBC7 Rxn#:2235 name: 5'-Phosphoribosylformylglycinamide:L-glutamine amido-ligase (ADP-forming) (No1) prev_Kcat:0.05 new_Kcat:5.0675 CC:0.26475 Err:1.0688% *************************************************************** Fitting sigma factor....................... Done! Saving simulation results files... File successfully saved. Sigma factor (fitted for growth on glucose): 0.3 ============= Saving models: ============= Saving eciSM966v1.0.0: 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 eciSM966_batchv1.0.0: 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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