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ModelSEED / Model-SEED-core

The Model SEED is a tool for building, curating, and analyzing gonome-scale metabolic models. Visit the Model SEED homepage for installation instructions and full feature documentation.
http://bionet.mcs.anl.gov/index.php/Model_SEED_Homepage
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Error Running mdl-autocomplete #159

Open aabest opened 12 years ago

aabest commented 12 years ago

We are trying to run the mdl-autocomplete command are are getting an error on one of our installations of ModelSEED. Works on other installations.

Here is the error:

Turing:~/Desktop/ModelSEED/Model-SEED-core/workspace/public/Shew5> mdl-autocomplete Seed211586.9.1?Complete?1 mdlautocomplete Creating problem directory: 14 Creating list of inactive reactions: /Users/student/Desktop/ModelSEED/Model-SEED-core/data/ReactionDB/MFAToolkitOutputFiles/14/InactiveModelReactions.txt Printing gapfilling parameters in : /Users/student/Desktop/ModelSEED/Model-SEED-core/data/ReactionDB/MFAToolkitOutputFiles/14/CompleteGapfillingParameters.txt Running runFBAStudy Using problem directory: 14 Creating the model file: /Users/student/Desktop/ModelSEED/Model-SEED-core/data/ReactionDB/MFAToolkitOutputFiles/14/Seed211586.9.1.tbl Creating biochemistry provenance files Running FBA mkdir: /Users/student/Desktop/ModelSEED/Model-SEED-core/data/ReactionDB/MFAToolkitOutputFiles/14/MFAOutput: File exists sh: line 1: 38146 Segmentation fault: 11 /Users/student/Desktop/ModelSEED/Model-SEED-core/software/mfatoolkit/bin/mfatoolkit resetparameter "MFA input directory" /Users/student/Desktop/ModelSEED/Model-SEED-core/data/ReactionDB/ parameterfile "../Parameters/ProductionMFA.txt" parameterfile "../Parameters/GapFilling.txt" parameterfile "/Users/student/Desktop/ModelSEED/Model-SEED-core/data/ReactionDB/MFAToolkitOutputFiles/14/CompleteGapfillingParameters.txt" parameterfile "/Users/student/Desktop/ModelSEED/Model-SEED-core/data/ReactionDB/MFAToolkitOutputFiles/14/AddnlFBAParameters.txt" LoadCentralSystem "/Users/student/Desktop/ModelSEED/Model-SEED-core/data/ReactionDB/MFAToolkitOutputFiles/14/Seed211586.9.1.tbl" > "/Users/student/Desktop/ModelSEED/Model-SEED-core/logs/fba-14.log" Parsing results Finished runFBAStudy Whoops! We encountered an unrecoverable error.

Gapfilling of model Seed211586.9.1 failed!

View error using the "ms-lasterror" command.

Have you updated recently? ( git pull ) Have you changed your configuration? ( ms-config )

If you are still having problems, please submit a ticket copying the contents of the error file printed above to:

https://github.com/ModelSEED/Model-SEED-core/issues/new

Thanks! Turing:~/Desktop/ModelSEED/Model-SEED-core/workspace/public/Shew5> ms-lasterror mslasterror Last error printed to file:

/Users/student/Desktop/ModelSEED/Model-SEED-core/.errors/error-i6IFc

Error text printed below:

ModelDriver encountered an unrecoverable error:

""Gapfilling of model Seed211586.9.1 failed!"" at /Users/student/Desktop/ModelSEED/Model-SEED-core/lib/ModelSEED/utilities.pm line 97
    ModelSEED::utilities::ERROR('Gapfilling of model Seed211586.9.1 failed!') called at /Users/student/Desktop/ModelSEED/Model-SEED-core/lib/ModelSEED/FIGMODEL/FIGMODELmodel.pm line 2083
    ModelSEED::FIGMODEL::FIGMODELmodel::completeGapfilling('ModelSEED::FIGMODEL::FIGMODELmodel=HASH(0x7ff9db5d0c78)', 'HASH(0x7ff9db5d0ca8)') called at /Users/student/Desktop/ModelSEED/Model-SEED-core/lib/ModelSEED/ModelDriver.pm line 1847
    ModelSEED::ModelDriver::mdlautocomplete('ModelSEED::ModelDriver=HASH(0x7ff9db5cd140)', 'mdlautocomplete', 'Seed211586.9.1', 'Complete', 1) called at /Users/student/Desktop/ModelSEED/Model-SEED-core/lib/ModelSEED/ModelDriver.pl line 131
    main::__ANON__() called at /System/Library/Perl/Extras/5.12/Try/Tiny.pm line 76
    eval {...} called at /System/Library/Perl/Extras/5.12/Try/Tiny.pm line 67
    Try::Tiny::try('CODE(0x7ff9db5cd218)', 'Try::Tiny::Catch=REF(0x7ff9db5cd0b0)') called at /Users/student/Desktop/ModelSEED/Model-SEED-core/lib/ModelSEED/ModelDriver.pl line 135
    require /Users/student/Desktop/ModelSEED/Model-SEED-core/lib/ModelSEED/ModelDriver.pl called at /Users/student/Desktop/ModelSEED/Model-SEED-core/config//ModelSEEDbootstrap.pm line 24
    main::run() called at -e line 3

Model-SEED-core revision: b029bdfc35b338b0b0869b5ee766514bcc16cfa9

samseaver commented 12 years ago

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

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

aabest commented 12 years ago

Hi Sam,

I am attaching the log file.

Thanks,

Aaron

On Thu, Jun 7, 2012 at 1:10 AM, samseaver < reply@reply.github.com

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:

https://github.com/ModelSEED/Model-SEED-core/issues/159#issuecomment-6168981

samseaver commented 12 years ago

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.

aabest commented 12 years ago

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;;

aabest commented 12 years ago

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

samseaver commented 12 years ago

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 reply@reply.github.com 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

Reply to this email directly or view it on GitHub: https://github.com/ModelSEED/Model-SEED-core/issues/159#issuecomment-6211078

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 samseaver@gmail.com (773) 796-7144

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