update/eciSM966/2022 07 03 22 07/2022 07 03 22 07 09

[automator-metatlas]

update eciSM966 based on 2022-07-03-22-07

MATLAB is selecting SOFTWARE OPENGL rendering.


      _____   _____   _____   _____     _____     |
     /  ___| /  _  \ |  _  \ |  _  \   / ___ \    |   COnstraint-Based Reconstruction and Analysis
     | |     | | | | | |_| | | |_| |  | |___| |   |   The COBRA Toolbox - 2022
     | |     | | | | |  _  { |  _  /  |  ___  |   |
     | |___  | |_| | | |_| | | | \ \  | |   | |   |   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: /home/m/ecModels-dependencies/gurobi951/linux64/matlab
   - [----] 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 8465 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 eciSM9662022-07-03-22-07:
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_batch2022-07-03-22-07:
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.