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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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Segmentation fault with new biomass #165

Open aabest opened 12 years ago

aabest commented 12 years ago

Any ideas what might be causing this? We have just updated and switched to a new biomass file for the model.

Thanks!

mdlautocomplete Creating problem directory: 359 Creating list of inactive reactions: /Users/student/Desktop/ModelSEED/Model-SEED-Core/data/ReactionDB/MFAToolkitOutputFiles/359/InactiveModelReactions.txt Printing gapfilling parameters in : /Users/student/Desktop/ModelSEED/Model-SEED-Core/data/ReactionDB/MFAToolkitOutputFiles/359/CompleteGapfillingParameters.txt Running runFBAStudy Using problem directory: 359 Creating the model file: /Users/student/Desktop/ModelSEED/Model-SEED-Core/data/ReactionDB/MFAToolkitOutputFiles/359/Seed211586.18.906.tbl Creating biochemistry provenance files Running FBA sh: line 1: 8682 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/359/CompleteGapfillingParameters.txt" parameterfile "/Users/student/Desktop/ModelSEED/Model-SEED-Core/data/ReactionDB/MFAToolkitOutputFiles/359/AddnlFBAParameters.txt" LoadCentralSystem "/Users/student/Desktop/ModelSEED/Model-SEED-Core/data/ReactionDB/MFAToolkitOutputFiles/359/Seed211586.18.906.tbl" > "/Users/student/Desktop/ModelSEED/Model-SEED-Core/logs/fba-359.log" Parsing results Finished runFBAStudy Whoops! We encountered an unrecoverable error.

Gapfilling of model Seed211586.18.906 failed!

View error using the "ms-lasterror" command.

OUTPUT of ms-lasterror:

Last error printed to file:

/Users/student/Desktop/ModelSEED/Model-SEED-Core/.errors/error-mbG7R

Error text printed below:

ModelDriver encountered an unrecoverable error:

""Gapfilling of model Seed211586.18.906 failed!"" at /Users/student/Desktop/ModelSEED/Model-SEED-Core/lib/ModelSEED/utilities.pm line 97
    ModelSEED::utilities::ERROR('Gapfilling of model Seed211586.18.906 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(0x7f882d687518)', 'HASH(0x7f882d6040f8)') called at /Users/student/Desktop/ModelSEED/Model-SEED-Core/lib/ModelSEED/ModelDriver.pm line 2163
    ModelSEED::ModelDriver::mdlautocomplete('ModelSEED::ModelDriver=HASH(0x7f882b032a68)', 'mdlautocomplete', 'Seed211586.18.906', '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(0x7f882d67a8d8)', 'Try::Tiny::Catch=REF(0x7f882b0329d8)') 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: 14bff21b7665f91b71220c572bec66f171512b13

samseaver commented 12 years ago

A seg fault can happen if you didn't attach the biomass to the model, I've made this mistake before.

./mdl-loadbiomass can be used to load a biomass into the database, but it must also be used along with the -Model switch to attach the biomass to the model of choice.