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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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GapFilling in local environment #47

Closed samseaver closed 13 years ago

samseaver commented 13 years ago

I'm getting a generic error:

StringDBTable:loadFromFile:could not open table file StringDBTable:get_object:no hash exists for query attribute StringDBTable:get_object:no hash exists for query attribute

It seems that StringDB.cpp in mfatoolkit is getting the wrong filename.

After a bit of debugging, I've found that the command that is run is:

/Users/seaver/Software/ModelSEEDCore/software/mfatoolkit/bin/mfatoolkit resetparameter "MFA input directory" /Users/seaver/Software/ModelSEEDCore/data/ReactionDB/ parameterfile "../Parameters/ProductionMFA.txt" parameterfile "../Parameters/GapFilling.txt" parameterfile "/Users/seaver/Software/ModelSEEDCore/data/ReactionDB/MFAToolkitOutputFiles/2098275/CompleteGapfillingParameters.txt" parameterfile "/Users/seaver/Software/ModelSEEDCore/data/ReactionDB/MFAToolkitOutputFiles/2098275/AddnlFBAParameters.txt" LoadCentralSystem "/Users/seaver/Software/ModelSEEDCore/data/ReactionDB/MFAToolkitOutputFiles/2098275/iJR904.45632.tbl" > "/Users/seaver/Software/ModelSEEDCore/logs/fba-2098275.log"

and its attempting to run this command from

/Users/seaver/Software/ModelSEEDCore

Its my belief that it cannot find some of the parameter files properly.

samseaver commented 13 years ago

I believe this has since been fixed