Error Running mdl-autocomplete about model-seed-core HOT 6 OPEN

Can you send me the log file, as shown in Run_MFAToolkit.sh:

/Users/student/Desktop/ModelSEED/Model-SEED-core/logs/fba-14.log

from model-seed-core.

Hi Sam,

I am attaching the log file.

Thanks,

Aaron

On Thu, Jun 7, 2012 at 1:10 AM, samseaver <
[email protected]

wrote:

Can you send me the log file, as shown in Run_MFAToolkit.sh:

/Users/student/Desktop/ModelSEED/Model-SEED-core/logs/fba-14.log

---

Reply to this email directly or view it on GitHub:

#159 (comment)

from model-seed-core.

I think I know what the problem is.

Can you double-check your model in:

/Users/student/Desktop/ModelSEED/Model-SEED-core/data/ReactionDB/MFAToolkitOutputFiles/14/Seed211586.9.1.tbl

to see if it has a biomass reaction?

I know that one problem we get is that the code seg faults if the model does not have a biomass reaction. We never did implement a check for this to say "You don't have a biomass reaction", so it just farts on you and quits.

===Update===

Allow me to correct myself. It correctly says there is no biomass reaction if you load a fresh model. However, if you re-load a model file, then it doesn't realize that a biomass reaction is missing, leading to the seg-fault.

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It appears that there is the following line in the .tbl file. This indicates biomass present, correct?

Turing:~/Desktop/ModelSEED/Model-SEED-core/workspace/AaronB/Shew5>
grep -i "bio" /Users/student/Desktop/ModelSEED/Model-SEED-core/data/ReactionDB/MFAToolkitOutputFiles/14/Seed211586.9.1.tbl
bio00170;=>;c;BOF;NONE;1;;

from model-seed-core.

It appears that the mfatoolkit was not rebuilt after an ms-update. When I did "ms-update" it said that the MFAToolkit was up to date. But I moved it out of the way (i.e., renamed to Model-SEED-core/software/mfatoolkit/Linux/mfatoolkit.bk), which forced a rebuild, and got a new mfatoolkit that is much bigger and now works.

-rwxrwxr-x 1 student staff 15564068 Jun 8 15:21 mfatoolkit
-rwxrwxr-x 1 student staff 1570392 May 22 09:31 mfatoolkit.bk

from model-seed-core.

Ah, that's interesting. I've never used ms-update, so clearly here
there's an issue with recognizing that the source files have been
updated and need to be re-compiled.

On Fri, Jun 8, 2012 at 2:26 PM, aabest
[email protected]
wrote:

It appears that the mfatoolkit was not rebuilt after an ms-update. When I did "ms-update" it said that the MFAToolkit was up to date. But I moved it out of the way (i.e., renamed to Model-SEED-core/software/mfatoolkit/Linux/mfatoolkit.bk), which forced a rebuild, and got a new mfatoolkit that is much bigger and now works.

-rwxrwxr-x  1 student  staff  15564068 Jun  8 15:21 mfatoolkit
-rwxrwxr-x  1 student  staff   1570392 May 22 09:31 mfatoolkit.bk

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Reply to this email directly or view it on GitHub:
#159 (comment)

Postdoctoral Fellow
Mathematics and Computer Science Division
Argonne National Laboratory
9700 S. Cass Avenue
Argonne, IL 60439

http://www.linkedin.com/pub/sam-seaver/0/412/168
[email protected]
(773) 796-7144

"We shall not cease from exploration
And the end of all our exploring
Will be to arrive where we started
And know the place for the first time."
   --T. S. Eliot

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