Error using readCbModel()

Michel Lavoie

unread,

May 13, 2017, 7:36:21 PM5/13/17

to COBRA Toolbox

Hello,

I tried to read several valid SBML files with the function readCbModel() using the CobraToolbox in MATLAB. However, no matter what SBML file I tried to read, I kept getting the following three error messages:

Error using convertSBMLToCobra

Too many input arguments.

Error in readCbModel>readSBMLCbModel (line 184)

model = convertSBMLToCobra(modelSBML,defaultBound,compSymbolList,compNameList);

Error in readCbModel (line 132)

model = readSBMLCbModel([fileName '.xml'],defaultBound,compSymbolList,compNameList);

Note that all the SBML files I try to read have been previously validated to work well. My question is similar to the question of Amornpan Klanchui (posted on 12 february) (object : Cobra Toolbox: Error readCbModel with valid sbml file). However, I could not see an answer to the question of M. Klanchui. Could you please tell me what I could do to fix the problem?

Thank you,

Michel

Thomas Pfau

unread,

May 15, 2017, 1:03:54 AM5/15/17

to cobra-...@googlegroups.com

Hi Michel,

Which version of the toolbox are you using? readSBMLCbModel is removed from the readCbModel function since over a year. Could you please install the current version of the toolbox and the requirements detailed here :

https://github.com/opencobra/cobratoolbox/blob/master/.github/REQUIREMENTS.md

and here:

https://github.com/opencobra/cobratoolbox#installation

Best

Thomas

--

---
You received this message because you are subscribed to the Google Groups "COBRA Toolbox" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cobra-toolbo...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

-- 
Université du Luxembourg
Faculté des Sciences, de la Technologie et de la Communication
Campus Belval, Biotech II 115
6 avenue du Swing
L-4367 Belvaux
Tel: (+352) 46 66 44 5309
Email: thoma...@uni.lu

Michel Lavoie

unread,

Jul 20, 2017, 11:22:42 PM7/20/17

to COBRA Toolbox

Thank you very much Thomas for your answer.

I have installed the current version of the Cobra toolbox, initialized it (initCobraToolbox), and tested all (TestAll) functions. However, I got some error messages when I tested with testAll(). Regarding my question about SBML file conversion into a Cobra file, I stil get error messages when I try to convert a valid SBML file into a matlab cobra file.

I consistently get the following error messages :

Error using TranslateSBML

Too many input arguments

USAGE: [model, (errors), (version)] = TranslateSBML((filename), (validateFlag), (verboseFlag))

Error in readSBML (line 31)

modelSBML = TranslateSBML(fileName,0,0,[1 1]);

Error in readCbModel (line 206)

model = readSBML(fileName,defaultBound);

Could you please tell me how I can convert a SBML file (expressed as . xml) to a Cobra file (.m) ?

Thank you very much for your support,

Michel

Laurent Heirendt

unread,

Jul 21, 2017, 1:54:19 AM7/21/17

to COBRA Toolbox

Hi,

May you post here the output of >> generateSystemConfigReport ?

Thanks,

Laurent

Michel Lavoie

unread,

Jul 21, 2017, 8:08:29 AM7/21/17

to COBRA Toolbox

Hi Laurent ,

Here is the output of >> generateSystemConfigReport. Thanks for your help.

> ---------------------------------- SYSTEM CONFIGURATION REPORT ----------------------------------

_____ _____ _____ _____ _____ |

/ ___| / _ \ | _ \ | _ \ / ___ \ | COnstraint-Based Reconstruction and Analysis

| | | | | | | |_| | | |_| | | |___| | | The COBRA Toolbox - 2017

| | | | | | | _ { | _ / | ___ | |

| |___ | |_| | | |_| | | | \ \ | | | | | Documentation:

\_____| \_____/ |_____/ |_| \_\ |_| |_| | http://opencobra.github.io/cobratoolbox

|

> Checking if git is installed ... Done.

> Checking if the repository is tracked using git ... Done.

> Checking if curl is installed ... (not installed).

> Checking if remote can be reached ... (unsuccessful - no internet connection).

> Adding all the files of The COBRA Toolbox ... Done.

> Define CB map output... set to svg.

> Retrieving models ... > The URL https://raw.github.com/snmendoz/Models/master/AntCore.mat cannot be reached.

> The URL http://bigg.ucsd.edu/static/models/iIT341.xml cannot be reached.

> The URL https://webdav-r3lab.uni.lu/public/msp/AGORA/sbml/Abiotrophia_defectiva_ATCC_49176.xml cannot be reached.

> The URL http://gcrg.ucsd.edu/sites/default/files/Attachments/Images/InSilicoOrganisms/yeast/Sc_iND750_flux1.xml cannot be reached.

> The URL http://gcrg.ucsd.edu/sites/default/files/Attachments/Images/downloads/Ecoli_core/ecoli_core_model.mat cannot be reached.

> The URL http://gcrg.ucsd.edu/sites/default/files/Attachments/Images/downloads/Ecoli_core/modelReg.mat cannot be reached.

> The URL http://bigg.ucsd.edu/static/models/iAF1260.mat cannot be reached.

> The URL http://bigg.ucsd.edu/static/models/iJO1366.mat cannot be reached.

> The URL https://webdav-r3lab.uni.lu/public/msp/AGORA/mat/Abiotrophia_defectiva_ATCC_49176.mat cannot be reached.

> The URL https://webdav-r3lab.uni.lu/public/msp/AGORA/mat/Acidaminococcus_fermentans_DSM_20731.mat cannot be reached.

> The URL https://webdav-r3lab.uni.lu/public/msp/AGORA/mat/Acidaminococcus_intestini_RyC_MR95.mat cannot be reached.

> The URL https://webdav-r3lab.uni.lu/public/msp/AGORA/mat/Acidaminococcus_sp_D21.mat cannot be reached.

> The URL https://webdav-r3lab.uni.lu/public/msp/AGORA/mat/Acinetobacter_calcoaceticus_PHEA_2.mat cannot be reached.

> The URL http://systemsbiology.ucsd.edu/sites/default/files/Attachments/Images/InSilicoOrganisms/Ecoli/Ecoli_SBML/msb4100155-s6.zip cannot be reached.

> The URL https://static-content.springer.com/esm/art%3A10.1186%2F1752-0509-5-8/MediaObjects/12918_2010_598_MOESM2_ESM.ZIP cannot be reached.

> The URL https://wwwen.uni.lu/content/download/72953/917521/file/download.zip cannot be reached.

> The URL https://vmh.uni.lu/files/Recon2.v04.mat_.zip cannot be reached.

> The URL https://wwwen.uni.lu/content/download/72949/917505/file/Human%20cardiac%20myocyte%20mitochondrial%20metabolic%20reconstruction_cardiac_mit_glcuptake_atpmax.mat.zip cannot be reached.

Done.

> Configuring solver environment variables ...

- [----] ILOG_CPLEX_PATH : --> set this path manually after installing the solver ( see instructions )

- [*---] GUROBI_PATH: C:\gurobi702\win64\matlab

- [----] TOMLAB_PATH : --> set this path manually after installing the solver ( see instructions )

- [----] MOSEK_PATH : --> set this path manually after installing the solver ( see instructions )

Done.

> Checking available solvers and solver interfaces ... Done.

> Setting default solvers ... Done.

> Saving the MATLAB path ... Done.

- The MATLAB path was saved in the default location.

> Summary of available solvers and solver interfaces

Support LP MILP QP MIQP NLP

----------------------------------------------------------------------

cplex_direct active 0 0 0 0 -

dqqMinos active 0 - - - -

glpk active 1 1 - - -

gurobi active 1 1 1 1 -

ibm_cplex active 0 0 0 - -

matlab active 1 - - - 1

mosek active 0 0 0 - -

pdco active 1 - 1 - -

quadMinos active 0 - - - 0

tomlab_cplex active 0 0 0 0 -

qpng passive - - 1 - -

tomlab_snopt passive - - - - 0

gurobi_mex legacy 0 0 0 0 -

lindo_old legacy 0 - - - -

lindo_legacy legacy 0 - - - -

lp_solve legacy 1 - - - -

opti legacy 0 0 0 0 0

----------------------------------------------------------------------

Total - 5 2 3 1 1

+ Legend: - = not applicable, 0 = solver not compatible or not installed, 1 = solver installed.

> You can solve LP problems using: 'glpk' - 'gurobi' - 'matlab' - 'pdco' - 'lp_solve'

> You can solve MILP problems using: 'glpk' - 'gurobi'

> You can solve QP problems using: 'gurobi' - 'pdco' - 'qpng'

> You can solve MIQP problems using: 'gurobi'

> You can solve NLP problems using: 'matlab'

Elapsed time is 24.132318 seconds.

----------------------------------------------------------------------------------------------------

MATLAB Version: 9.1.0.441655 (R2016b)

MATLAB License Number: 310290

Operating System: Microsoft Windows 10 Famille Version 10.0 (Build 15063)

Java Version: Java 1.7.0_60-b19 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode

----------------------------------------------------------------------------------------------------

MATLAB Version 9.1 (R2016b)

Simulink Version 8.8 (R2016b)

Aerospace Toolbox Version 2.18 (R2016b)

Communications System Toolbox Version 6.3 (R2016b)

Computer Vision System Toolbox Version 7.2 (R2016b)

Control System Toolbox Version 10.1 (R2016b)

Curve Fitting Toolbox Version 3.5.4 (R2016b)

DSP System Toolbox Version 9.3 (R2016b)

Data Acquisition Toolbox Version 3.10 (R2016b)

Database Toolbox Version 7.0 (R2016b)

Financial Toolbox Version 5.8 (R2016b)

Fixed-Point Designer Version 5.3 (R2016b)

Fuzzy Logic Toolbox Version 2.2.24 (R2016b)

Global Optimization Toolbox Version 3.4.1 (R2016b)

HDL Verifier Version 5.1 (R2016b)

Image Acquisition Toolbox Version 5.1 (R2016b)

Image Processing Toolbox Version 9.5 (R2016b)

Instrument Control Toolbox Version 3.10 (R2016b)

MATLAB Coder Version 3.2 (R2016b)

MATLAB Compiler Version 6.3 (R2016b)

MATLAB Compiler SDK Version 6.3 (R2016b)

Mapping Toolbox Version 4.4 (R2016b)

Model Predictive Control Toolbox Version 5.2.1 (R2016b)

Neural Network Toolbox Version 9.1 (R2016b)

OPC Toolbox Version 4.0.2 (R2016b)

Optimization Toolbox Version 7.5 (R2016b)

Parallel Computing Toolbox Version 6.9 (R2016b)

Partial Differential Equation Toolbox Version 2.3 (R2016b)

RF Toolbox Version 3.1 (R2016b)

Robust Control Toolbox Version 6.2 (R2016b)

Signal Processing Toolbox Version 7.3 (R2016b)

Simscape Version 4.1 (R2016b)

Simscape Multibody Version 4.9 (R2016b)

Simscape Power Systems Version 6.6 (R2016b)

Simulink Coder Version 8.11 (R2016b)

Simulink Control Design Version 4.4 (R2016b)

Simulink Desktop Real-Time Version 5.3 (R2016b)

Simulink Real-Time Version 6.5 (R2016b)

Statistics and Machine Learning Toolbox Version 11.0 (R2016b)

Symbolic Math Toolbox Version 7.1 (R2016b)

System Identification Toolbox Version 9.5 (R2016b)

Wavelet Toolbox Version 4.17 (R2016b)

> Default shell :

> Version of shell : '--version' n'est pas reconnu en tant que commande interne

ou externe, un programme exécutable ou un fichier de commandes.

> Architecture : PCWIN64

> MATLAB folder : C:\Program Files\MATLAB\R2016b

> COBRA Toolbox root : C:\Users\Utilisateur\Documents\GitHub\cobratoolbox

> git version : git version 2.10.0.windows.1

> curl version : 'curl' n'est pas

> CBT_LP_SOLVER : gurobi

> CBT_MILP_SOLVER : gurobi

> CBT_QP_SOLVER : gurobi

> CBT_MIQP_SOLVER : gurobi

> CBT_NLP_SOLVER : matlab

> GUROBI_PATH : C:\gurobi702\win64\matlab

> ILOG_CPLEX_PATH :

> TOMLAB_PATH :

> MOSEK_PATH :

> ----------------------------------- END OF CONFIGURATION REPORT -----------------------------------

Laurent Heirendt

unread,

Jul 21, 2017, 8:57:21 AM7/21/17

to COBRA Toolbox

Hi,

The reason is that you didn't install Git Bash as explained here: https://github.com/opencobra/cobratoolbox/blob/master/docs/source/installation/requirements.md#what-if-my-system-is-not-properly-configured

The binaries for reading SBML files will not be downloaded unless you have Git Bash installed, especially the system tools (make sure that you select the third option during installation). If you already have Git Bash installed, uninstall and then reinstall the software.

Please let me know if this works.

Best,

Laurent

Michel Lavoie

unread,

Jul 21, 2017, 2:30:39 PM7/21/17

to COBRA Toolbox

Hi Laurent, I found the problem. Curl was not installed on my computer and hence, when I initialized and tested the Cobra toolbox with "tinitCobratoolbox" and "testAll", several files could not be downloaded on my computer and several functions of the Cobra toolbox did not work. Now, after having installed Curl , almost all tests were passed except five tests

'testFEA/testFEA'

'testSteadyCom/testSteadyCom'

'testWriteCbModel/testWriteCbModel'

'testXls2Model/testXls2Model'

'testPaint4Net/testPaint4Net'

The command readCbModel() appears to work now! Thank you very much for your help!

Regards, Michel

Laurent Heirendt

unread,

Jul 21, 2017, 2:48:40 PM7/21/17

to COBRA Toolbox

Hi,

Great to hear that it worked. Curl is installed as part of Git Bash, which is a requirement for the COBRA Toolbox on Windows.

I am not sure why these tests did not pass - do you mind attaching the output of >> testAll?

Best,

Laurent

Michel Lavoie

unread,

Jul 21, 2017, 8:05:57 PM7/21/17

to COBRA Toolbox

Hi Laurent,

The testing step (with the command " testAll" took more than 1 h and a half on my slow and old (i3, 2 ghz, PC) computer ! I can do another test and save the output for you (if my computer survive!) . Do you want only the end of the output or all the output?

Thanks,

Michel

Laurent Heirendt

unread,

Jul 22, 2017, 4:17:32 AM7/22/17

to COBRA Toolbox

Hi Michel,

Yes, testAll might take a while depending on the machine's specifications. If you can, it would be great to have all the output in order to see the error messages thrown for each test.

Thanks,

Laurent

Michel Lavoie

unread,

Jul 23, 2017, 7:08:25 AM7/23/17

to COBRA Toolbox

Hi Laurent, You may find attached the long output of testAll in a .txt file.

Michel

testCobraToolbox.txt

Mausmi Singh

unread,

May 12, 2022, 7:07:04 AM5/12/22

to COBRA Toolbox

Hi,

I'm getting error using readCbModel() command.

I tried uninstalling CobraToolbox. Also, I did all the troubleshooting mentioned in this thread. but nothing worked for me.

when I'm tried to load the model using readCbModel(), it's give some warning that excel is not installed and limit is 10000 reaction and then throwing this error.

I'm using MacBook Pro M1 chip. but when I used the same command readCbModel to load the model in windows it was perfectly working.

Error using xls2model (line 320)
Not all metabolites could be matched

Error in readCbModel (line 221)
model = xls2model(fileName, [], defaultBound);

Any help will be highly appreciated. Thank you.

kind regards,

Mausmi Singh

Thomas Pfau

unread,

May 13, 2022, 5:55:14 PM5/13/22

to cobra-...@googlegroups.com

Hi,

The problem is, that matlab doesn't like excel on *nix type systems, which includes mac.

There are a couple of options that can be used to still load the model:

1. Save it as a .mat file in Windows and load the .mat file with your mac.
2. Store it as an sbml and reload it on the mac.
3. install xlread (https://www.mathworks.com/matlabcentral/fileexchange/65824-xlread), and remove the whole isunix block in xls2model (113-126 along with the "end" in line 129) and replace xlsread by xlread.

Best

Thomas

To view this discussion on the web visit https://groups.google.com/d/msgid/cobra-toolbox/d17b4589-d85a-4828-9d93-33f8e7125a52n%40googlegroups.com.

Ronan M.T. Fleming

unread,

May 31, 2022, 7:05:28 AM5/31/22

to COBRA Toolbox

Hi Thomas/Masumi,
would one of you add
https://uk.mathworks.com/matlabcentral/fileexchange/65824-xlread to
cobratoolbox/external then edit xls2model and make a pull request?
Regards,
Ronan

> To view this discussion on the web visit https://groups.google.com/d/msgid/cobra-toolbox/5b38bd19-9681-030e-9305-4eb0aa2241e6%40thomaspfau.de.

--
--
Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
----------------------------------------------------------------------------
Associate Professor,
School of Medicine,
National University of Ireland, Galway.
&
Assistant Professor,
Division of Systems Biomedicine and Pharmacology,
Leiden Academic Centre for Drug Research,
Faculty of Science,
Leiden University.
https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming
&
H2020 Project Coordinator,
Systems Medicine of Mitochondrial Parkinson’s Disease,
http://sysmedpd.eu
----------------------------------------------------------------------------
Peer-reviewed publications: https://goo.gl/FZPG23
Mobile: +353 852 109 806
Skype: ronan.fleming
----------------------------------------------------------------------------
(This message is confidential and may contain privileged information.
It is intended for the named recipient only. If you receive it in
error please notify me and permanently delete the original message and
any copies.)

Reply all

Reply to author

Forward