Error while using FastGapFill

[Karan Kumar]

Dear all:

I am trying to run the FastgapFill command on my model and getting following error which is attached below:

tic; [consistModel,consistMatricesSUX,BlockedRxns] = prepareFastGapFill(model);

tpre=toc;

   651 Total reactions

   254 Reversible reactions.

   397 Irreversible reactions.

Error using load

Unable to read file 'KEGGMatrix'. No such file or directory.

Error in generateSUXComp (line 49)

    load KEGGMatrix

Error in prepareFastGapFill (line 86)

MatricesSUX = generateSUXComp(consistModel,dictionary, filename,blackList,listCompartments);

Please suggest, where am I wrong. And also how to resolve this issue.

Thanks and awaiting reply,

Karan.

[Ronan M.T. Fleming]

Hi Karan,
I confirm there is an issue with the code as testFastGapFill does not
complete correctly. Perhaps you can help to debug the problem?
Regards,
Ronan

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
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[Pritam Kundu]

Hi!

I have also encountered the same problem.

please suggest some way out.

Thank You.

Pritam

[Kristy Chang]

Dear All,

Was a solution ever found for this issue? I am still experiencing this issue. Thank you!

Best regards,

Kristy

[Kristy Chang]

The issue stems from the function 'prepareFastGapFill', but I cannot figure out what is missing from it. I would guess the function calls a Matrix ''KEGGMatrix' in a file that should be embedded into the function but is not being called. Was it accidentally deleted?

[Kristy Chang]

Tested the following to no avail:

Load in KEGG_dictionary.xls file from https://github.com/opencobra/COBRA.tutorials/tree/master/reconstruction/fastGapFill/example

dictionary_file= readtable('KEGG_dictionary.xls');

KEGGMatrix=table2array(dictionary_file)

[consistModel,consistMatricesSUX,BlockedRxns] = prepareFastGapFill(model)

I also tried manually substituting the dictionary as in:

[consistModel,consistMatricesSUX,BlockedRxns] = prepareFastGapFill(model,KEGGMatrix)

But it throws up the same error:

Error using load
Unable to read file 'KEGGMatrix'. No such file or directory.

Error in generateSUXComp (line 49)
    load KEGGMatrix

Error in prepareFastGapFill (line 86)
MatricesSUX = generateSUXComp(consistModel,dictionary, filename,blackList,listCompartments);

[RYTH DASGUPTA]

Hi all,

Was this issue resolved?
If not, is there another tool that can perform gap-filling for a metabolic model, or will the analogous function for prepareFastGapFill on CobraPy work?

Warm regards,

Ryth

[Thomas Pfau]

Hi,

I have put in a pull request too update fastGapFill. There were some changes that lead to it not creating relevant files if they were not existent but the flags were set.
Once that PR is in, I hope this should work again. At least the test runs again for me.

Best

Thomas

To view this discussion on the web visit https://groups.google.com/d/msgid/cobra-toolbox/46bf4674-1366-4d62-ab86-e1cfdf9ab87bn%40googlegroups.com.

[RYTH DASGUPTA]

Hi Thomas,

That is great news! Thank you very much.

Warm regards,

Ryth Dasgupta

To view this discussion on the web visit https://groups.google.com/d/msgid/cobra-toolbox/09a82410-2bc1-d8c3-cb49-960953c199eb%40thomaspfau.de.

[Nandini Kannoju]

Hello Prof. Fleming 

I'm working on flux balance analysis using a cobra tool box on the corynebacterium glutamicum ATCC 13032 model which has a lot of gaps in the metabolic pathway and trying to use the fastgapfill method. I'm taking the reference in this paper( 2014-Thiele-fastGapFill.pdf (googlegroups.com))  and example problem COBRA.tutorials/reconstruction/fastGapFill at master · opencobra/COBRA.tutorials · GitHub. I was having trouble while running the code and had few errors.  I have attached the screenshot of the error which i'm getting. Please help me in this regard to resolve this issue. 

And also the paper which I'm referring to was published in 2014. Do you have any papers published later where it will be useful for me to go through. 

[Nandini Kannoju]

Hello Prof. Ronan, 

Do you have any suggestions for alternative toolbox for fastgapfill ?

Thank you