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franciscozorrilla / metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
https://franciscozorrilla.github.io/metaGEM/
MIT License
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feat: develop rules for SMETANA global metrics #93

Closed franciscozorrilla closed 2 years ago

franciscozorrilla commented 2 years ago

Currently in the pipeline we focus on the SMETANA detailed algorithm, using the -d or --detailed flag to enumerate all possible interactions between species. However, when running the SMETANA global algorithm using the -g of --global to calculate MIP and MRO scores, errors/warnings typically arise resulting in one or more n/a value. To get values for the global metrics MIP and MRO, use the --cobra flag when building models with CarveMe and use the -- flavor ucsd flag with SMETANA.

Task: Develop rules for SMETANA global algorithm

franciscozorrilla commented 2 years ago

After some testing it looks like carving with the --fbc2 flag and running global simulation with --fbc2 flag will work fine