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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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Model loading #75

Closed alikpel closed 13 years ago

alikpel commented 13 years ago

After successful model loading

./fba-fva -model iJR904 doesn't work

Error log :

ModelDriver encountered an unrecoverable error:

""ModelSEED::FIGMODEL"" at /specific/disk1/home/alexnade/Model-SEED-core/lib/ModelSEED/FIGMODEL.pm line 139
    ModelSEED::FIGMODEL::FIGMODELERROR('ModelSEED::FIGMODEL', 'Model iJR904 not found in database!') called at /specific/disk1/home/alexnade/Model-SEED-core/lib/ModelSEED/ModelDriver.pm line 5644
    ModelSEED::ModelDriver::fbafva('ModelSEED::ModelDriver=HASH(0x3c1a1a8)', 'fbafva', 'HASH(0x3bf5c08)') called at /specific/disk1/home/alexnade/Model-SEED-core/lib/ModelSEED/ModelDriver.pl line 87
    main::__ANON__() called at /usr/share/perl5/Try/Tiny.pm line 76
    eval {...} called at /usr/share/perl5/Try/Tiny.pm line 67
    Try::Tiny::try('CODE(0x3c09dc0)', 'Try::Tiny::Catch=REF(0x3c0e158)') called at /specific/disk1/home/alexnade/Model-SEED-core/lib/ModelSEED/ModelDriver.pl line 91
    require /specific/disk1/home/alexnade/Model-SEED-core/lib/ModelSEED/ModelDriver.pl called at /specific/disk1/home/alexnade/Model-SEED-core/config//ModelSEEDbootstrap.pm line 20
    main::run() called at -e line 3

Model-SEED-core revision: a3c51c43c7a23fd5a58c2bcfb9adba1c1b860dbc

My Configuration file:

[Database]

type is either sqlite or mysql

type=sqlite

required for sqlite

filename=/specific/disk1/home/alexnade/Model-SEED-core/data/ModelDB/ModelDB.db

required for mysql

username=seed

password=seedxhs

host=localhost

socket=/var/run/mysqld/mysqld.sock

port=3306

[Optional] dataDirectory=/specific/disk1/home/alexnade/Model-SEED-core/data/

admin_users=admin1,admin2

[Optimizers] includeDirectoryGLPK=/usr/lib/ libraryDirectoryGLPK=/usr/include/

includeDirectoryCPLEX=/usr/local/lib/cplex121/include/

libraryDirectoryCPLEX=/usr/local/lib/cplex121/lib/x86-64_sles9.0_3.3/static_pic/

licenceDirectoryCPLEX=/usr/ilog/ilm/

Tnx, Alik

jamesclulow commented 13 years ago

Look in data/models/yourusername The model that you imported will have a tag behind it specific to your workspace. i.e. iJR904 is called iJR904.46352 in my case. You need to add that tag on when trying the fba commands.

jamesclulow commented 13 years ago

The error is coming from the fact that it cannot find the model that you imported under the name iJR904. 'Model iJR904 not found in database!'

alikpel commented 13 years ago

Great! added the suffix and it worked. tnx