some metabolicTasks_Essential Fail when running prepHumanModelForftINIT #809
yasamantaebi
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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.
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