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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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Low objective_value with the latest Carveme version #125

Closed juz4karen closed 3 years ago

juz4karen commented 3 years ago

Hi,

I found out model built with the latest version Carveme has a very different growth with the same sequence file.

Carveme 1.2.2 No. reactions: 2828 No. metabolites: 1734 No. genes: 1897 No. exchange reactions: 330 objective_value on M9: 0.16

Carveme 1.5.0 No. reactions: 2957 No. metabolites: 1824 No. genes: 1981 No. exchange reactions: 392 objective_value on M9: 0.92

Model was built carve genome.faa --fbc2 -g M9,LB -i M9 -o new_model.xml .

Hope to advise.

Regards, Karen

cdanielmachado commented 3 years ago

Hi Karen, this seems to be a common pattern reported by different users. I am trying to solve this.

By the way, did you accidentally swap the growth rates your example above?

juz4karen commented 3 years ago

oh sorry..latest version with lower growth.

Carveme 1.2.2 No. reactions: 2828 No. metabolites: 1734 No. genes: 1897 No. exchange reactions: 330 objective_value on M9: 0.92

Carveme 1.5.0 No. reactions: 2957 No. metabolites: 1824 No. genes: 1981 No. exchange reactions: 392 objective_value on M9: 0.16

juz4karen commented 3 years ago

Meanwhile, is that possible that I can download old version of Carveme?

cdanielmachado commented 3 years ago

Of course: pip install carveme==1.4.1

juz4karen commented 3 years ago

Will this overwrite with the existing version or a different installation? If no, how may I know if i'm using the 1.4.1 CarveMe build the model?

cdanielmachado commented 3 years ago

Better do pip uninstall carveme first just to be sure.

cdanielmachado commented 3 years ago

Should be solved in release 1.5.1, otherwise please re-open this issue.