Human-GEM
Human-GEM copied to clipboard
SysBioChalmers
some metabolicTasks_Essential Fail when running prepHumanModelForftINIT
Discussed in https://github.com/SysBioChalmers/Human-GEM/discussions/809
Originally posted by yasamantaebi March 6, 2024 I am trying to run ftINIT on the Human-Gem model. In prepData step, some essential tasks fail.Hence, it's not possible to run the next steps. I am using SCip solver for RAVEN because of the problem in reaching gurobi academic license. Here is the output of the prepHumanModelForftINIT function: Step 1: Gene rules Step 2: First simplification Step 3: Check tasks (~10 min) PASS: [ER] Aerobic rephosphorylation of ATP from glucose PASS: [ER] Aerobic rephosphorylation of GTP PASS: [ER] Aerobic rephosphorylation of CTP PASS: [ER] Aerobic rephosphorylation of UTP FAIL: [BS] ATP de novo synthesis PASS: [BS] CTP de novo synthesis FAIL: [BS] GTP de novo synthesis PASS: [BS] UTP de novo synthesis FAIL: [BS] dATP de novo synthesis PASS: [BS] dCTP de novo synthesis FAIL: [BS] dGTP de novo synthesis PASS: [BS] dTTP de novo synthesis PASS: [SU] Histidine uptake PASS: [SU] Isoleucine uptake PASS: [SU] Leucine uptake PASS: [SU] Lysine uptake PASS: [SU] Methionine uptake PASS: [SU] Phenylalanine uptake PASS: [SU] Threonine uptake PASS: [SU] Tryptophan uptake PASS: [SU] Valine uptake PASS: [IC] Glycerate 3-phosphate de novo synthesis PASS: [IC] Mitochondrial acetyl-CoA de novo synthesis PASS: [IC] Mitochondrial AKG de novo synthesis PASS: [IC] Erythrose 4-phosphate de novo synthesis PASS: [IC] Fructose 6-phosphate de novo synthesis PASS: [IC] Glyceraldehyde 3-phosphate de novo synthesis PASS: [IC] Glucose 6-phosphate de novo synthesis PASS: [IC] Mitochondrial oxaloacetate de novo synthesis PASS: [IC] Phosphoenolpyruvate de novo synthesis PASS: [IC] Pyruvate de novo synthesis PASS: [IC] Ribose 5-phosphate de novo synthesis PASS: [IC] Mitochondrial succinyl-CoA de novo synthesis PASS: [BS] Cholesterol de novo synthesis PASS: [BS] Protein synthesis from AAs PASS: [ER] Oxidative phosphorylation PASS: [ER] Oxidative decarboxylation PASS: [ER] Krebs cycle NADH PASS: [ER] Ubiquinol-to-proton PASS: [ER] Ubiquinol-to-ATP PASS: [SU] Beta oxidation of saturated FA FAIL: [SU] Beta oxidation of long-chain FA PASS: [SU] Beta oxidation of odd-chain FA PASS: [SU] Beta oxidation of unsaturated fatty acid (n-9) FAIL: [SU] Beta oxidation of unsaturated fatty acid (n-6) FAIL: [SU] Uptake and beta oxidation of all NEFAs PASS: [SU] Choline uptake PASS: [SU] Inositol uptake FAIL: [BS] Phosphatidylcholine de novo synthesis FAIL: [BS] Phosphatidylethanolamine de novo synthesis FAIL: [BS] Phosphatidylserine de novo synthesis FAIL: [BS] Phosphatidylinositol de novo synthesis PASS: [BS] Thiamin phosphorylation to TPP FAIL: [BS] Coenzyme A synthesis from pantothenate FAIL: [BS] FAD synthesis from riboflavin FAIL: [BS] Heme biosynthesis FAIL: [GR] Growth on Ham's media (biomass production) Step 4: Second simplification (~1 hour) Starting parallel pool (parpool) using the 'local' profile ... Connected to the parallel pool (number of workers: 4). Analyzing and transferring files to the workers ...done. Step 5: Final work IdleTimeout has been reached. Parallel pool using the 'local' profile is shutting down.
Hi, I have tried using different solvers today to get prepData. I noticed that when using the gurobi solver, all tasks passed, but when using the glpk solver, 7 tasks(dTTP de novo synthesis, Protein synthesis from AAs, Ubiquinol-to-ATP, Beta oxidation of odd-chain FA, Beta oxidation of unsaturated fatty acid (n-9), Beta oxidation of unsaturated fatty acid (n-6) and Growth on Ham's media (biomass production)) failed. Combined with your result of using the SCIP solver (15 fail), I think it is caused by the solver. Since Human-GEM contains more than 10,000 reactions, there may be certain requirements on the performance of the solver, so I suggest you change the gurobi solver to run ftINIT.
As mentioned above, human-GEM is a large model, while ftINIT is a complex approach, so it indeed heavily depends on an well-functioning solver. Gurobi is superior in that aspect, so its use is highly recommended for these tasks.
I can however not replicate your observation, using scip here is terribly slow, but all the tasks pass.
Could you please report your RAVEN version; MATLAB version; and operating system version?
I am closing this issue since we don't get reply for one month. But feel free to reopen this if you still have this issue.
