search

opencobra / memote

memote – the genome-scale metabolic model test suite
https://memote.readthedocs.io/
Apache License 2.0
128 stars 28 forks source link

The current solver interface glpk doesn't support setting the optimality tolerance #724

Closed helenaherand closed 3 years ago

helenaherand commented 3 years ago

Yesterday, I ran into "The current solver interface glpk doesn't support setting the optimality tolerance" when running memote in the terminal. I tried to change the interface to CPLEX and Gurobi (glpk) by the solver option but cplex did not seem to be a valid interface and "--solver glpk" did not solve the issue. Does anyone know why glpk does not support setting the optimality tolerance and/or how I may solve it?

helenaherand commented 3 years ago

memote report snapshot Human-GEM.xml Scaling... A: min|aij| = 1.000e+00 max|aij| = 1.000e+00 ratio = 1.000e+00 Problem data seem to be well scaled The current solver interface glpk doesn't support setting the optimality tolerance. ============================= test session starts ============================== platform linux -- Python 3.6.7, pytest-6.2.5, py-1.10.0, pluggy-1.0.0 rootdir: /home/helena plugins: anyio-3.3.4 collected 191 items / 1 skipped / 190 selected

../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py . [ 0%] ..FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFFF.F..F....FFF.FFF.FFFF.. [ 34%] ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_basic.py . [ 34%] .....FF.......F.F.F.FF [ 46%] ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py . [ 46%] FFFFFFFFFFF.FFFFF.............FFFFFFFFFFF.......FFFFFF [ 74%] ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_consistency.py . [ 75%] ..ssssssssssssssssFFFFFF.FFF [ 90%] ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_essentiality.py s [ 90%] [ 90%] ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_growth.py s [ 91%] [ 91%] ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_matrix.py . [ 91%] F.. [ 93%] ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_sbml.py . [ 93%] . [ 94%] ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_sbo.py F [ 94%] FFFFFFFss. [100%]

=============================== warnings summary =============================== .local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_consistency[MAR00021] .local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_consistency[MAR04413] .local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_consistency[MAR09931] .local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_consistency[MAR09932] .local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_consistency[MAR12140] .local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_consistency[MAR13082] /home/helena/.local/lib/python3.6/site-packages/cobra/core/metabolite.py:135: UserWarning: The element 'R' does not appear in the periodic table warn("The element %s does not appear in the periodic table" % e)

-- Docs: https://docs.pytest.org/en/stable/warnings.html =========================== short test summary info ============================ FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_overview[pubchem.compound] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_overview[kegg.compound] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_overview[seed.compound] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_overview[inchikey] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_overview[inchi] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_overview[chebi] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_overview[hmdb] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_overview[reactome] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_overview[metanetx.chemical] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_overview[bigg.metabolite] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_overview[biocyc] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_reaction_annotation_overview[rhea] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_reaction_annotation_overview[kegg.reaction] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_reaction_annotation_overview[seed.reaction] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_reaction_annotation_overview[metanetx.reaction] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_reaction_annotation_overview[bigg.reaction] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_reaction_annotation_overview[reactome] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_reaction_annotation_overview[ec-code] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_reaction_annotation_overview[brenda] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_reaction_annotation_overview[biocyc] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_gene_product_annotation_overview[refseq] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_gene_product_annotation_overview[uniprot] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_gene_product_annotation_overview[ecogene] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_gene_product_annotation_overview[kegg.genes] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_gene_product_annotation_overview[ncbigi] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_gene_product_annotation_overview[ncbigene] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_gene_product_annotation_overview[ncbiprotein] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_gene_product_annotation_overview[ccds] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_gene_product_annotation_overview[hprd] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_gene_product_annotation_overview[asap] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_wrong_ids[kegg.compound] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_wrong_ids[seed.compound] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_wrong_ids[inchikey] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_wrong_ids[chebi] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_wrong_ids[hmdb] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_wrong_ids[reactome] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_wrong_ids[metanetx.chemical] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_wrong_ids[biocyc] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_reaction_annotation_wrong_ids[seed.reaction] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_reaction_annotation_wrong_ids[brenda] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_reaction_annotation_wrong_ids[biocyc] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_gene_product_annotation_wrong_ids[refseq] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_gene_product_annotation_wrong_ids[ecogene] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_gene_product_annotation_wrong_ids[kegg.genes] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_gene_product_annotation_wrong_ids[ncbigi] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_gene_product_annotation_wrong_ids[ncbiprotein] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_gene_product_annotation_wrong_ids[ccds] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_gene_product_annotation_wrong_ids[hprd] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_gene_product_annotation_wrong_ids[asap] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_basic.py::test_gene_protein_reaction_rule_presence FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_basic.py::test_ngam_presence FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_basic.py::test_transport_reaction_gpr_presence FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_basic.py::test_find_unique_metabolites FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_basic.py::test_find_reactions_with_partially_identical_annotations FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_basic.py::test_find_reactions_with_identical_genes FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_basic.py::test_find_medium_metabolites FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_consistency[MAR00021] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_consistency[MAR04413] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_consistency[MAR09931] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_consistency[MAR09932] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_consistency[MAR12140] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_consistency[MAR13082] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_default_production[MAR00021] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_default_production[MAR04413] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_default_production[MAR09931] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_default_production[MAR09932] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_default_production[MAR12140] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_open_production[MAR00021] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_open_production[MAR04413] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_open_production[MAR09931] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_open_production[MAR09932] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_open_production[MAR12140] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_gam_in_biomass[MAR00021] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_gam_in_biomass[MAR04413] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_gam_in_biomass[MAR09931] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_gam_in_biomass[MAR09932] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_gam_in_biomass[MAR12140] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_gam_in_biomass[MAR13082] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_fast_growth_default[MAR00021] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_fast_growth_default[MAR04413] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_fast_growth_default[MAR09931] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_fast_growth_default[MAR09932] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_fast_growth_default[MAR12140] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_essential_precursors_not_in_biomass[MAR00021] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_essential_precursors_not_in_biomass[MAR04413] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_essential_precursors_not_in_biomass[MAR09931] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_essential_precursors_not_in_biomass[MAR09932] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_essential_precursors_not_in_biomass[MAR12140] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_essential_precursors_not_in_biomass[MAR13082] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_consistency.py::test_reaction_charge_balance FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_consistency.py::test_reaction_mass_balance FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_consistency.py::test_blocked_reactions FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_consistency.py::test_find_stoichiometrically_balanced_cycles FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_consistency.py::test_find_orphans FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_consistency.py::test_find_deadends FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_consistency.py::test_find_metabolites_not_produced_with_open_bounds FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_consistency.py::test_find_metabolites_not_consumed_with_open_bounds FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_consistency.py::test_find_reactions_unbounded_flux_default_condition FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_matrix.py::test_number_independent_conservation_relations FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_sbo.py::test_metabolite_sbo_presence FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_sbo.py::test_reaction_sbo_presence FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_sbo.py::test_gene_sbo_presence FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_sbo.py::test_metabolic_reaction_specific_sbo_presence FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_sbo.py::test_transport_reaction_specific_sbo_presence FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_sbo.py::test_metabolite_specific_sbo_presence FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_sbo.py::test_gene_specific_sbo_presence FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_sbo.py::test_exchange_specific_sbo_presence ===== 107 failed, 64 passed, 21 skipped, 6 warnings in 2660.59s (0:44:20) ====== Writing snapshot report to 'index.html'.

carrascomj commented 3 years ago

Hello Helena!

It is just a warning, you can safely ignore it. Some solvers, like glpk, in some versions of cobrapy (which ultimately depends on the version of optlang it is using) do not implement or do not expose setting the tolerance of the solver and that generates a warning.

By the way, in order to use cplex or gurobi, you have to install them first separately. Both provide academic licenses.

helenaherand commented 3 years ago

Thanks, carrascomj!