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cdanielmachado / smetana

SMETANA: a tool to analyse interactions in microbial communities
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Model loading Issue with Smetana #7

Closed NTDevika closed 4 years ago

NTDevika commented 4 years ago

I am encountering the following error upon running smetana (Input single species models generated from Carveme). I tried giving even the test files (uploaded in the githubpage), but encountering the same error. Can you please help me out t sort this issue?

command used smetana ec_glc_ko.xml ec_nh4_ko.xml --flavor cobra SMETANA_Error

cdanielmachado commented 4 years ago

In this case, you are using our example models which are using fbc2 flavor, not cobra. Please remove the flavor option (fbc2 is the default).

NTDevika commented 4 years ago

I am using smetana to generate the cross fed metabolites. Input Command smetana Lactobacillus_paracasei_ATCC_334.xml V_harveyi_QT520.xml --mediadb constrained_media_comp.tsv --flavor cobra Output community medium size mip mro all complete 2 n/a 0.7692307692307693

why is the mip score showing n/a? Further in smetana is their anyway , the program will output the list or name of cross-fed metabolites. Thank You!!

cdanielmachado commented 4 years ago

MIP is calculated by comparing the number of nutrients required when the species grow together vs growing alone. If they cannot grow alone, then MIP cannot be calculated.