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error in mergeTwoModels

Open PejmanS opened this issue 6 years ago • 24 comments

I have faced with this error in mgPipe Error using mergeTwoModels>mergeFields (line 232) Subscript indices must either be real positive integers or logicals

what is that for?

  • [x] Tried to solve the issue on my own
  • [x] Retried to run my code with the latest version of The COBRA Toolbox
  • [x] Checked that a similar issue has not already been opened

PejmanS avatar Sep 24 '19 19:09 PejmanS

Could you provide the models you used?

tpfau avatar Sep 24 '19 19:09 tpfau

I have used AGORA models, pan models of AGORA and embl-GEM models.

PejmanS avatar Sep 24 '19 19:09 PejmanS

Is there any solution?

PejmanS avatar Sep 28 '19 08:09 PejmanS

@almut-heinken

PejmanS avatar Oct 04 '19 08:10 PejmanS

@PejmanS Please address such issues to me right away, otherwise I won't see them. I am not encountering this issue so I am not sure what is happening. I assume it is because of a problem with the gene rules. What version of AGORA are you using?

almut-heinken avatar Oct 04 '19 11:10 almut-heinken

@almut-heinken I'm using AGORA 1.03 This error occured on line 232 of mergeTwoModels. There is this code on this line: default = modelNew.(fields2{i})(end); I think the (end) is wrong here, is it correct?

On Fri, Oct 4, 2019, 2:52 PM almut-heinken [email protected] wrote:

@PejmanS https://github.com/PejmanS Please address such issues to me right away, otherwise I won't see them. I am not encountering this issue so I am not sure what is happening. I assume it is because of a problem with the gene rules. What version of AGORA are you using?

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PejmanS avatar Oct 04 '19 11:10 PejmanS

@tpfau

PejmanS avatar Oct 08 '19 18:10 PejmanS

Could you provide the exact sequence of commands from loading the models up to the error? And which models exactly you used (optimally the model files)?Am 08.10.2019 21:46 schrieb PejmanS [email protected]:@tpfau

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tpfau avatar Oct 09 '19 07:10 tpfau

@PejmanS @tpfau I am guessing it has something to do with the COBRA Toolbox now crashing on minor synthax errors in the grRules field. readCbModel also does not work on certain models anymore. I will have a look, but I am traveling this week, so I cannot do it before next Monday.

almut-heinken avatar Oct 09 '19 08:10 almut-heinken

@tpfau @almut-heinken autoStat =

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Error in mergeTwoModels (line 124) modelNew = mergeFields(modelNew,model1,model2,'comps');

Error in fastSetupCreator (line 224) parfor k=1:halfdim

Error in mgPipe (line 91) setup=fastSetupCreator(models, strains, {},objre)

Error in initMgPipe (line 165) mgPipe

Error in startMgPipe (line 46) [init,modPath,toolboxPath,resPath,dietFilePath,abunFilePath,indInfoFilePath,objre,figForm,numWorkers,autoFix,compMod,rDiet,extSolve,fvaType,autorun]= initMgPipe(modPath, toolboxPath, resPath, dietFilePath, abunFilePath,indInfoFilePath, objre, figForm, numWorkers, autoFix, compMod, rDiet,extSolve,fvaType,autorun);

This is the line 232 of mergeTwoModels: default = modelNew.(fields2{i})(end)

At first i supposed that (end) is the prolem, when i deleted it and ran the mgPipe, error occured at 234th line that it is not A (:) = B, it means it passed this line for 'Subscript indices must either be real positive integers or logicals' error.

After that i ran a test with a data just by pan models of AGORA. It was ok and passed this line without any error!

@tpfau I have used AGORA models, pan models of AGORA (species and genus levels) and embl GEMS ( https://github.com/cdanielmachado/embl_gems ). Do you wnat the list? they are about 345 models.

PejmanS avatar Oct 09 '19 15:10 PejmanS

I was talking about the script, not the error message.

I.e. what are you

Other than that: Did you use readCbModel to load the models?

If not, could you run verifyModel on the models to see if they are valid models?r

@almut-heinken:

Well, if there are syntax errors in grRules, than those models are not valid, and could fail at different places of the toolbox so they should be corrected. I did add a hardcoded fix for the recon2 mat file which is invalid as well as it is so abundantly used, but we can't hard code fixes for all invalid models in the toolbox.

On 09/10/2019 17:02, PejmanS wrote:

@tpfau https://github.com/tpfau @almut-heinken https://github.com/almut-heinken autoStat =

|1 |

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Error in mergeTwoModels (line 124) modelNew = mergeFields(modelNew,model1,model2,'comps');

Error in fastSetupCreator (line 224) parfor k=1:halfdim

Error in mgPipe (line 91) setup=fastSetupCreator(models, strains, {},objre)

Error in initMgPipe (line 165) mgPipe

Error in startMgPipe (line 46) [init,modPath,toolboxPath,resPath,dietFilePath,abunFilePath,indInfoFilePath,objre,figForm,numWorkers,autoFix,compMod,rDiet,extSolve,fvaType,autorun]= initMgPipe(modPath, toolboxPath, resPath, dietFilePath, abunFilePath,indInfoFilePath, objre, figForm, numWorkers, autoFix, compMod, rDiet,extSolve,fvaType,autorun);

This is the line 232 of mergeTwoModels: default = modelNew.(fields2{i})(end)

At first i supposed that (end) is the prolem, when i deleted it and ran the mgPipe, error occured at 234th line that it is not A (:) = B, it means it passed this line for 'Subscript indices must either be real positive integers or logicals' error.

After that i ran a test with a data just by pan models of AGORA. It was ok and passed this line without any error!

@tpfau https://github.com/tpfau I have used AGORA models, pan models of AGORA (species and genus levels) and embl GEMS ( https://github.com/cdanielmachado/embl_gems ). Do you wnat the list? they are about 345 models.

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tpfau avatar Oct 09 '19 17:10 tpfau

@tpfau Sorry, do you want all of scripts of mgPipe? i just ran mgPipe, and this error occured automatically on mergeTwoModels function. I didn't change anything after updated COBRA.

yes i have read all models by readCbModel and they were ok. Should i verifyModel in all fields?

PejmanS avatar Oct 09 '19 17:10 PejmanS

Hmmm

thats odd then.

I'll try to have a look, but I can't currently give an estimate as to when I'll be able to address this.

Could you try to figure out if the problem occurs whe

On 09/10/2019 19:49, PejmanS wrote:

@tpfau https://github.com/tpfau Sorry, do you want all of scripts of mgPipe? i just ran mgPipe, and this error occured automatically on mergeTwoModels function. I didn't change anything after updated COBRA.,

yes i have read all models by readCbModel and they were ok. Should i verifyModel in all fields?

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tpfau avatar Oct 09 '19 17:10 tpfau

Sorry, for that half message.

Could you try to figure out if it happens with a particular model?

Since it worked with the AGORA models, I assume that the problem is either in some code reading the other models, or in one of them. Or its an odd border case that we did not consider.

On 09/10/2019 19:49, PejmanS wrote:

@tpfau https://github.com/tpfau Sorry, do you want all of scripts of mgPipe? i just ran mgPipe, and this error occured automatically on mergeTwoModels function. I didn't change anything after updated COBRA.

yes i have read all models by readCbModel and they were ok. Should i verifyModel in all fields?

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tpfau avatar Oct 09 '19 17:10 tpfau

I think you are right. Because i did it just by pan AGORA models and was ok. But is there any way to solve it?

PejmanS avatar Oct 09 '19 18:10 PejmanS

I found the issue. Its a bug in mergeTwoModels when combining models with the comps field that just never appeared, because the agora models don't have this field. I put in a PR (#1508) to fix it. Until that is in, you can just do those changed manually (its just 2 lines that need to be adapted).

tpfau avatar Oct 09 '19 18:10 tpfau

@tpfau Yes, I already identifed the three AGORA models that fail in readCbModel. This causes createPanModels to crash. I will replace the three models on the VMH website as soon as possible. @PejmanS Are you using AGORA and EBML GEMs in the same study? This will probably cause issues since the reaction nomenclature doesn't agree.

almut-heinken avatar Oct 09 '19 21:10 almut-heinken

@almut-heinken Yes, I'm testing that. Did you check that pan models are compatible with AGORA 1.03? We talked about that in another issue.

PejmanS avatar Oct 09 '19 21:10 PejmanS

@PejmanS Yes, I will also submit a pull request with an update to createPanModels next week that ensures the pan-models don't have futile cycles.

almut-heinken avatar Oct 09 '19 21:10 almut-heinken

@tpfau Thanks, it works now. But i have faced with another error: Error using coupleRxnList2Rxn (line 66) In an assignment A(:) = B, the number of elements in A and B must be the same.

Error in createPersonalizedModel (line 50) parfor k = 2:(patNumb + 1)

Error in mgPipe (line 106) [createdModels]=createPersonalizedM

@almut-heinken Is it what you believed about using EMBL GEMs?

PejmanS avatar Oct 10 '19 10:10 PejmanS

@tpfau @almut-heinken

PejmanS avatar Oct 16 '19 21:10 PejmanS

Can you provide a minimal example (i.e. a minimal set of models) where this error occurs?

Just from this error I really have no idea, what might be happening.

On 10/10/2019 12:27, PejmanS wrote:

@tpfau https://github.com/tpfau Thanks, it works now. But i have faced with another error: Error using coupleRxnList2Rxn (line 66) In an assignment A(:) = B, the number of elements in A and B must be the same.

Error in createPersonalizedModel (line 50) parfor k = 2:(patNumb + 1)

Error in mgPipe (line 106) [createdModels]=createPersonalizedM

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tpfau avatar Oct 19 '19 11:10 tpfau

Can you provide a minimal example (i.e. a minimal set of models) where this error occurs? Just from this error I really have no idea, what might be happening. … On 10/10/2019 12:27, PejmanS wrote: @tpfau https://github.com/tpfau Thanks, it works now. But i have faced with another error: Error using coupleRxnList2Rxn (line 66) In an assignment A(:) = B, the number of elements in A and B must be the same. Error in createPersonalizedModel (line 50) parfor k = 2:(patNumb + 1) Error in mgPipe (line 106) [createdModels]=createPersonalizedM — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1505?email_source=notifications&email_token=ACMCYKSJCQZ43VFR5MOQ773QN37SJA5CNFSM4I2DYDEKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEA3XRIY#issuecomment-540506275>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACMCYKS3TSNNO52LBIILEDTQN37SJANCNFSM4I2DYDEA.

Hi I reduced models and samples. but this error has occured again.

PejmanS avatar Dec 02 '19 17:12 PejmanS

Hi @PejmanS, please provide us with the models you are trying to join and the code for joining them. Otherwise, it is hard to say what is going on. Best, Almut

almut-heinken avatar Dec 03 '19 10:12 almut-heinken