Hi.. First I would like to thank you for providing such an amazing tool! I am new to computational studies and also to MICOM, so I am sorry in advance if this question is not makes much sense
When I use grow function I encounter with the error of:
"All numerical optimizations failed. This indicates a problem with the solver or numerical instabilities. Check that you have CPLEX or Gurobi installed. You may also increase the abundance cutoff to create simpler models."
from micom.workflows import grow
from micom.workflows import grow
from micom.qiime_formats import load_qiime_medium
data=pd.read_excel('data.xlsx')
print(data)
agora_data_try = pd.read_csv('meta.tsv', sep='\t')
manifest = build(data, out_folder="/home/dgenc/new_env/models", model_db='agora103_genus.qza', cutoff=0.000001, threads=8,solver='cplex')
print(manifest)
medium = load_qiime_medium("western_diet_gut.qza")
print(medium)
res = grow(manifest, model_folder="models", medium=medium, tradeoff=0.5, threads=8, presolve=True)
print(res)
If I am able to pass this error, then I get the following error:
This can often be fixed by enabling presolve, choosing more permissive atol and rtol arguments, or by checking that medium fluxes are > atol.
Thank you so much for you help!!