R for Metagenomics: MaAslin2
Ryan McMinds
install Maaslin2
MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.
Find the Masslin2 Referance Manuel here
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Maaslin2")## Warning: package(s) not installed when version(s) same as current; use `force = TRUE` to
## re-install: 'Maaslin2'library(Maaslin2)load the pathway abundance file
abundances <- read.table('data/preterm_metagenomes_pathabundance.tsv', header=T, sep='\t', quote='', comment.char='')
colnames(abundances) <- sub('_.*','',colnames(abundances))
# remove the stratified rows (so we focus on total pathway abundance, not pathway abundance within particular species)
abundances_filt <- abundances[grep('|',abundances[,1],invert=T,fixed=T),]
rownames(abundances_filt) <- abundances_filt[,1]
abundances_filt <- abundances_filt[,-1]load the sample metadata and make sure the variables have the right types
meta <- read.table('data/meta_data_sra_acc.tsv', header=T, sep='\t')
rownames(meta) <- meta$Sample
# make sure the metadata table has samples in the same order as the abundances table
meta <- meta[colnames(abundances_filt),]
#
meta$Gender <- as.factor(meta$Gender)
# there are three factor levels for 'group', and it makes most biological sense to compare to the baseline of 'Term'
meta$Group <- relevel(as.factor(meta$Group), 'Term')
meta$Individual <- as.factor(meta$Individual)
meta$DeliveryMode <- as.factor(meta$DeliveryMode)
meta$EnteralFeeds_2mo <- as.factor(meta$EnteralFeeds_2mo)
# some values of 'Breastmilk' have extra spaces in them for some reason, so we'll clean those up
levels(meta$EnteralFeeds_2mo)[gsub(' ', '', levels(meta$EnteralFeeds_2mo)) == 'Breastmilk'] <- 'Breastmilk'fit <- Maaslin2(abundances_filt, meta, 'outputs/maaslin_functional', random_effects='Individual', fixed_effects=c('Gender','Group'), reference='Group,Term')## [1] "Warning: Deleting existing log file: outputs/maaslin_functional/maaslin2.log"
## 2021-07-28 09:35:04 INFO::Writing function arguments to log file
## 2021-07-28 09:35:04 INFO::Verifying options selected are valid
## 2021-07-28 09:35:04 INFO::Determining format of input files
## 2021-07-28 09:35:04 INFO::Input format is data samples as columns and metadata samples as rows
## 2021-07-28 09:35:04 INFO::Formula for random effects: expr ~ (1 | Individual)
## 2021-07-28 09:35:04 INFO::Formula for fixed effects: expr ~ Gender + Group
## 2021-07-28 09:35:04 INFO::Filter data based on min abundance and min prevalence
## 2021-07-28 09:35:04 INFO::Total samples in data: 429
## 2021-07-28 09:35:04 INFO::Min samples required with min abundance for a feature not to be filtered: 42.900000
## 2021-07-28 09:35:04 INFO::Total filtered features: 121
## 2021-07-28 09:35:04 INFO::Filtered feature names from abundance and prevalence filtering: X7ALPHADEHYDROX.PWY..cholate.degradation..bacteria..anaerobic., ALL.CHORISMATE.PWY..superpathway.of.chorismate.metabolism, CATECHOL.ORTHO.CLEAVAGE.PWY..catechol.degradation.to..beta..ketoadipate, CRNFORCAT.PWY..creatinine.degradation.I, DHGLUCONATE.PYR.CAT.PWY..glucose.degradation..oxidative., LIPASYN.PWY..phospholipases, LYSINE.DEG1.PWY..L.lysine.degradation.XI..mammalian., MANNOSYL.CHITO.DOLICHOL.BIOSYNTHESIS..protein.N.glycosylation..eukaryotic..high.mannose., NADSYN.PWY..NAD.biosynthesis.II..from.tryptophan., P124.PWY..Bifidobacterium.shunt, P163.PWY..L.lysine.fermentation.to.acetate.and.butanoate, P165.PWY..superpathway.of.purines.degradation.in.plants, P221.PWY..octane.oxidation, PWY.101..photosynthesis.light.reactions, PWY.1622..formaldehyde.assimilation.I..serine.pathway., PWY.2201..folate.transformations.I, PWY.2221..Entner.Doudoroff.pathway.III..semi.phosphorylative., PWY.3661..glycine.betaine.degradation.I, PWY.3801..sucrose.degradation.II..sucrose.synthase., PWY.4321..L.glutamate.degradation.IV, PWY.5004..superpathway.of.L.citrulline.metabolism, PWY.5028..L.histidine.degradation.II, PWY.5044..purine.nucleotides.degradation.I..plants., PWY.5067..glycogen.biosynthesis.II..from.UDP.D.Glucose., PWY.5079..L.phenylalanine.degradation.III, PWY.5080..very.long.chain.fatty.acid.biosynthesis.I, PWY.5088..L.glutamate.degradation.VIII..to.propanoate., PWY.5129..sphingolipid.biosynthesis..plants., PWY.5179..toluene.degradation.V..aerobic...via.toluene.cis.diol., PWY.5180..toluene.degradation.I..aerobic...via.o.cresol., PWY.5181..toluene.degradation.III..aerobic...via.p.cresol., PWY.5182..toluene.degradation.II..aerobic...via.4.methylcatechol., PWY.5273..p.cumate.degradation, PWY.5381..pyridine.nucleotide.cycling..plants., PWY.5417..catechol.degradation.III..ortho.cleavage.pathway., PWY.5431..aromatic.compounds.degradation.via..beta..ketoadipate, PWY.5514..UDP.N.acetyl.D.galactosamine.biosynthesis.II, PWY.5651..L.tryptophan.degradation.to.2.amino.3.carboxymuconate.semialdehyde, PWY.5692..allantoin.degradation.to.glyoxylate.II, PWY.5870..ubiquinol.8.biosynthesis..eukaryotic., PWY.5871..ubiquinol.9.biosynthesis..eukaryotic., PWY.5872..ubiquinol.10.biosynthesis..eukaryotic., PWY.5873..ubiquinol.7.biosynthesis..eukaryotic., PWY.5994..palmitate.biosynthesis.I..animals.and.fungi., PWY.6074..zymosterol.biosynthesis, PWY.6075..ergosterol.biosynthesis.I, PWY.6138..CMP.N.acetylneuraminate.biosynthesis.I..eukaryotes., PWY.6145..superpathway.of.sialic.acids.and.CMP.sialic.acids.biosynthesis, PWY.6185..4.methylcatechol.degradation..ortho.cleavage., PWY.622..starch.biosynthesis, PWY.6263..superpathway.of.menaquinol.8.biosynthesis.II, PWY.6307..L.tryptophan.degradation.X..mammalian..via.tryptamine., PWY.6309..L.tryptophan.degradation.XI..mammalian..via.kynurenine., PWY.6313..serotonin.degradation, PWY.6318..L.phenylalanine.degradation.IV..mammalian..via.side.chain., PWY.6351..D.myo.inositol..1.4.5..trisphosphate.biosynthesis, PWY.6435..4.hydroxybenzoate.biosynthesis.V, PWY.6470..peptidoglycan.biosynthesis.V...beta..lactam.resistance., PWY.6562..norspermidine.biosynthesis, PWY.6596..adenosine.nucleotides.degradation.I, PWY.6598..sciadonate.biosynthesis, PWY.6660..2.heptyl.3.hydroxy.4.1H..quinolone.biosynthesis, PWY.6662..superpathway.of.quinolone.and.alkylquinolone.biosynthesis, PWY.6749..CMP.legionaminate.biosynthesis.I, PWY.6785..hydrogen.production.VIII, PWY.6837..fatty.acid.beta.oxidation.V..unsaturated..odd.number..di.isomerase.dependent., PWY.6876..isopropanol.biosynthesis, PWY.6981..chitin.biosynthesis, PWY.7007..methyl.ketone.biosynthesis, PWY.7031..protein.N.glycosylation..bacterial., PWY.7090..UDP.2.3.diacetamido.2.3.dideoxy..alpha..D.mannuronate.biosynthesis, PWY.7094..fatty.acid.salvage, PWY.7118..chitin.degradation.to.ethanol, PWY.7165..L.ascorbate.biosynthesis.VI..engineered.pathway., PWY.7200..superpathway.of.pyrimidine.deoxyribonucleoside.salvage, PWY.7235..superpathway.of.ubiquinol.6.biosynthesis..eukaryotic., PWY.7245..superpathway.NAD.NADP...NADH.NADPH.interconversion..yeast., PWY.7268..NAD.NADP.NADH.NADPH.cytosolic.interconversion..yeast., PWY.7270..L.methionine.salvage.cycle.II..plants., PWY.7283..wybutosine.biosynthesis, PWY.7286..7..3.amino.3.carboxypropyl..wyosine.biosynthesis, PWY.7288..fatty.acid..beta..oxidation..peroxisome..yeast., PWY.7290..Escherichia.coli.serotype.O86.O.antigen.biosynthesis, PWY.7294..xylose.degradation.IV, PWY.7312..dTDP.D..beta..fucofuranose.biosynthesis, PWY.7316..dTDP.N.acetylviosamine.biosynthesis, PWY.7332..superpathway.of.UDP.N.acetylglucosamine.derived.O.antigen.building.blocks.biosynthesis, PWY.7337..10.cis.heptadecenoyl.CoA.degradation..yeast., PWY.7338..10.trans.heptadecenoyl.CoA.degradation..reductase.dependent..yeast., PWY.7345..superpathway.of.anaerobic.sucrose.degradation, PWY.7371..1.4.dihydroxy.6.naphthoate.biosynthesis.II, PWY.7384..anaerobic.energy.metabolism..invertebrates..mitochondrial., PWY.7385..1.3.propanediol.biosynthesis..engineered., PWY.7389..superpathway.of.anaerobic.energy.metabolism..invertebrates., PWY.7391..isoprene.biosynthesis.II..engineered., PWY.7411..superpathway.of.phosphatidate.biosynthesis..yeast., PWY.7420..monoacylglycerol.metabolism..yeast., PWY.7431..aromatic.biogenic.amine.degradation..bacteria., PWY.7528..L.methionine.salvage.cycle.I..bacteria.and.plants., PWY.7546..diphthamide.biosynthesis..eukaryotes., PWY.7616..methanol.oxidation.to.carbon.dioxide, PWY.7619..juniperonate.biosynthesis, PWY0.881..superpathway.of.fatty.acid.biosynthesis.I..E..coli., PWY1G.0..mycothiol.biosynthesis, PWY3DJ.35471..L.ascorbate.biosynthesis.IV, PWY3O.19..ubiquinol.6.biosynthesis.from.4.hydroxybenzoate..eukaryotic., PWY3O.355..stearate.biosynthesis.III..fungi., PWY66.367..ketogenesis, PWY66.375..leukotriene.biosynthesis, PWY66.388..fatty.acid..alpha..oxidation.III, PWY66.391..fatty.acid..beta..oxidation.VI..peroxisome., RUMP.PWY..formaldehyde.oxidation.I, SPHINGOLIPID.SYN.PWY..sphingolipid.biosynthesis..yeast., TEICHOICACID.PWY..teichoic.acid..poly.glycerol..biosynthesis, THREOCAT.PWY..superpathway.of.L.threonine.metabolism, TRIGLSYN.PWY..diacylglycerol.and.triacylglycerol.biosynthesis, TYRFUMCAT.PWY..L.tyrosine.degradation.I, UDPNACETYLGALSYN.PWY..UDP.N.acetyl.D.glucosamine.biosynthesis.II, URDEGR.PWY..superpathway.of.allantoin.degradation.in.plants, URSIN.PWY..ureide.biosynthesis, VALDEG.PWY..L.valine.degradation.I
## 2021-07-28 09:35:04 INFO::Running selected normalization method: TSS
## 2021-07-28 09:35:05 INFO::Total filtered features with variance filtering: 0
## 2021-07-28 09:35:05 INFO::Filtered feature names from variance filtering:
## 2021-07-28 09:35:05 INFO::Applying z-score to standardize continuous metadata
## 2021-07-28 09:35:05 INFO::Running selected transform method: LOG
## 2021-07-28 09:35:05 INFO::Running selected analysis method: LM
## 2021-07-28 09:35:05 INFO::Fitting model to feature number 1, UNMAPPED
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 2, UNINTEGRATED
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 3, X1CMET2.PWY..N10.formyl.tetrahydrofolate.biosynthesis
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 4, X3.HYDROXYPHENYLACETATE.DEGRADATION.PWY..4.hydroxyphenylacetate.degradation
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 5, AEROBACTINSYN.PWY..aerobactin.biosynthesis
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 6, ALLANTOINDEG.PWY..superpathway.of.allantoin.degradation.in.yeast
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 7, ANAEROFRUCAT.PWY..homolactic.fermentation
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 8, ANAGLYCOLYSIS.PWY..glycolysis.III..from.glucose.
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 9, ARG.POLYAMINE.SYN..superpathway.of.arginine.and.polyamine.biosynthesis
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 10, ARGDEG.PWY..superpathway.of.L.arginine..putrescine..and.4.aminobutanoate.degradation
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 11, ARGININE.SYN4.PWY..L.ornithine.de.novo..biosynthesis
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 12, ARGORNPROST.PWY..arginine..ornithine.and.proline.interconversion
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 13, ARGSYN.PWY..L.arginine.biosynthesis.I..via.L.ornithine.
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 14, ARGSYNBSUB.PWY..L.arginine.biosynthesis.II..acetyl.cycle.
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 15, ARO.PWY..chorismate.biosynthesis.I
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 16, ASPASN.PWY..superpathway.of.L.aspartate.and.L.asparagine.biosynthesis
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 17, AST.PWY..L.arginine.degradation.II..AST.pathway.
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 18, BIOTIN.BIOSYNTHESIS.PWY..biotin.biosynthesis.I
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 19, BRANCHED.CHAIN.AA.SYN.PWY..superpathway.of.branched.amino.acid.biosynthesis
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 20, CALVIN.PWY..Calvin.Benson.Bassham.cycle
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 21, CENTFERM.PWY..pyruvate.fermentation.to.butanoate
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 22, CITRULBIO.PWY..L.citrulline.biosynthesis
## 2021-07-28 09:35:06 INFO::Fitting model to feature number 23, COA.PWY.1..coenzyme.A.biosynthesis.II..mammalian.
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 24, COA.PWY..coenzyme.A.biosynthesis.I
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 25, COBALSYN.PWY..adenosylcobalamin.salvage.from.cobinamide.I
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 26, COLANSYN.PWY..colanic.acid.building.blocks.biosynthesis
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 27, COMPLETE.ARO.PWY..superpathway.of.aromatic.amino.acid.biosynthesis
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 28, DAPLYSINESYN.PWY..L.lysine.biosynthesis.I
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 29, DENOVOPURINE2.PWY..superpathway.of.purine.nucleotides.de.novo.biosynthesis.II
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 30, DTDPRHAMSYN.PWY..dTDP.L.rhamnose.biosynthesis.I
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 31, ECASYN.PWY..enterobacterial.common.antigen.biosynthesis
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 32, ENTBACSYN.PWY..enterobactin.biosynthesis
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 33, FAO.PWY..fatty.acid..beta..oxidation.I
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 34, FASYN.ELONG.PWY..fatty.acid.elongation....saturated
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 35, FASYN.INITIAL.PWY..superpathway.of.fatty.acid.biosynthesis.initiation..E..coli.
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 36, FERMENTATION.PWY..mixed.acid.fermentation
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 37, FOLSYN.PWY..superpathway.of.tetrahydrofolate.biosynthesis.and.salvage
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 38, FUC.RHAMCAT.PWY..superpathway.of.fucose.and.rhamnose.degradation
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 39, FUCCAT.PWY..fucose.degradation
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 40, GALACT.GLUCUROCAT.PWY..superpathway.of.hexuronide.and.hexuronate.degradation
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 41, GALACTARDEG.PWY..D.galactarate.degradation.I
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 42, GALACTUROCAT.PWY..D.galacturonate.degradation.I
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 43, GLCMANNANAUT.PWY..superpathway.of.N.acetylglucosamine..N.acetylmannosamine.and.N.acetylneuraminate.degradation
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 44, GLUCARDEG.PWY..D.glucarate.degradation.I
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 45, GLUCARGALACTSUPER.PWY..superpathway.of.D.glucarate.and.D.galactarate.degradation
## 2021-07-28 09:35:07 INFO::Fitting model to feature number 46, GLUCONEO.PWY..gluconeogenesis.I
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 47, GLUCOSE1PMETAB.PWY..glucose.and.glucose.1.phosphate.degradation
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 48, GLUCUROCAT.PWY..superpathway.of..beta..D.glucuronide.and.D.glucuronate.degradation
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 49, GLUDEG.I.PWY..GABA.shunt
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 50, GLUTORN.PWY..L.ornithine.biosynthesis
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 51, GLYCOCAT.PWY..glycogen.degradation.I..bacterial.
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 52, GLYCOGENSYNTH.PWY..glycogen.biosynthesis.I..from.ADP.D.Glucose.
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 53, GLYCOL.GLYOXDEG.PWY..superpathway.of.glycol.metabolism.and.degradation
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 54, GLYCOLYSIS.E.D..superpathway.of.glycolysis.and.Entner.Doudoroff
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 55, GLYCOLYSIS.TCA.GLYOX.BYPASS..superpathway.of.glycolysis..pyruvate.dehydrogenase..TCA..and.glyoxylate.bypass
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 56, GLYCOLYSIS..glycolysis.I..from.glucose.6.phosphate.
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 57, GLYOXYLATE.BYPASS..glyoxylate.cycle
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 58, GOLPDLCAT.PWY..superpathway.of.glycerol.degradation.to.1.3.propanediol
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 59, HCAMHPDEG.PWY..3.phenylpropanoate.and.3..3.hydroxyphenyl.propanoate.degradation.to.2.oxopent.4.enoate
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 60, HEME.BIOSYNTHESIS.II..heme.biosynthesis.I..aerobic.
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 61, HEMESYN2.PWY..heme.biosynthesis.II..anaerobic.
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 62, HEXITOLDEGSUPER.PWY..superpathway.of.hexitol.degradation..bacteria.
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 63, HISDEG.PWY..L.histidine.degradation.I
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 64, HISTSYN.PWY..L.histidine.biosynthesis
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 65, HOMOSER.METSYN.PWY..L.methionine.biosynthesis.I
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 66, HSERMETANA.PWY..L.methionine.biosynthesis.III
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 67, ILEUSYN.PWY..L.isoleucine.biosynthesis.I..from.threonine.## boundary (singular) fit: see ?isSingular## 2021-07-28 09:35:08 INFO::Fitting model to feature number 68, KDO.NAGLIPASYN.PWY..superpathway.of..Kdo.2.lipid.A.biosynthesis
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 69, KETOGLUCONMET.PWY..ketogluconate.metabolism
## 2021-07-28 09:35:08 INFO::Fitting model to feature number 70, LACTOSECAT.PWY..lactose.and.galactose.degradation.I
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 71, LPSSYN.PWY..superpathway.of.lipopolysaccharide.biosynthesis
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 72, MET.SAM.PWY..superpathway.of.S.adenosyl.L.methionine.biosynthesis
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 73, METHGLYUT.PWY..superpathway.of.methylglyoxal.degradation
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 74, METSYN.PWY..L.homoserine.and.L.methionine.biosynthesis
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 75, NAD.BIOSYNTHESIS.II..NAD.salvage.pathway.II
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 76, NAGLIPASYN.PWY..lipid.IVA.biosynthesis
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 77, NONMEVIPP.PWY..methylerythritol.phosphate.pathway.I
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 78, NONOXIPENT.PWY..pentose.phosphate.pathway..non.oxidative.branch.
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 79, OANTIGEN.PWY..O.antigen.building.blocks.biosynthesis..E..coli.
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 80, ORNARGDEG.PWY..superpathway.of.L.arginine.and.L.ornithine.degradation
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 81, ORNDEG.PWY..superpathway.of.ornithine.degradation
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 82, P105.PWY..TCA.cycle.IV..2.oxoglutarate.decarboxylase.
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 83, P108.PWY..pyruvate.fermentation.to.propanoate.I
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 84, P122.PWY..heterolactic.fermentation
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 85, P125.PWY..superpathway.of..R.R..butanediol.biosynthesis
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 86, P161.PWY..acetylene.degradation
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 87, P162.PWY..L.glutamate.degradation.V..via.hydroxyglutarate.
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 88, P164.PWY..purine.nucleobases.degradation.I..anaerobic.
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 89, P185.PWY..formaldehyde.assimilation.III..dihydroxyacetone.cycle.
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 90, P23.PWY..reductive.TCA.cycle.I
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 91, P4.PWY..superpathway.of.L.lysine..L.threonine.and.L.methionine.biosynthesis.I
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 92, P42.PWY..incomplete.reductive.TCA.cycle
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 93, P441.PWY..superpathway.of.N.acetylneuraminate.degradation
## 2021-07-28 09:35:09 INFO::Fitting model to feature number 94, P461.PWY..hexitol.fermentation.to.lactate..formate..ethanol.and.acetate
## 2021-07-28 09:35:10 INFO::Fitting model to feature number 95, P562.PWY..myo.inositol.degradation.I
## 2021-07-28 09:35:10 INFO::Fitting model to feature number 96, PANTO.PWY..phosphopantothenate.biosynthesis.I
## 2021-07-28 09:35:10 INFO::Fitting model to feature number 97, PANTOSYN.PWY..pantothenate.and.coenzyme.A.biosynthesis.I
## 2021-07-28 09:35:10 INFO::Fitting model to feature number 98, PENTOSE.P.PWY..pentose.phosphate.pathway
## 2021-07-28 09:35:10 INFO::Fitting model to feature number 99, PEPTIDOGLYCANSYN.PWY..peptidoglycan.biosynthesis.I..meso.diaminopimelate.containing.## boundary (singular) fit: see ?isSingular## 2021-07-28 09:35:10 INFO::Fitting model to feature number 100, PHOSLIPSYN.PWY..superpathway.of.phospholipid.biosynthesis.I..bacteria.
## 2021-07-28 09:35:10 INFO::Fitting model to feature number 101, POLYAMINSYN3.PWY..superpathway.of.polyamine.biosynthesis.II
## 2021-07-28 09:35:10 INFO::Fitting model to feature number 102, POLYAMSYN.PWY..superpathway.of.polyamine.biosynthesis.I
## 2021-07-28 09:35:10 INFO::Fitting model to feature number 103, POLYISOPRENSYN.PWY..polyisoprenoid.biosynthesis..E..coli.
## 2021-07-28 09:35:10 INFO::Fitting model to feature number 104, PPGPPMET.PWY..ppGpp.biosynthesis
## 2021-07-28 09:35:10 INFO::Fitting model to feature number 105, PROTOCATECHUATE.ORTHO.CLEAVAGE.PWY..protocatechuate.degradation.II..ortho.cleavage.pathway.
## 2021-07-28 09:35:10 INFO::Fitting model to feature number 106, PRPP.PWY..superpathway.of.histidine..purine..and.pyrimidine.biosynthesis
## 2021-07-28 09:35:10 INFO::Fitting model to feature number 107, PWY.1042..glycolysis.IV..plant.cytosol.
## 2021-07-28 09:35:10 INFO::Fitting model to feature number 108, PWY.1269..CMP.3.deoxy.D.manno.octulosonate.biosynthesis.I
## 2021-07-28 09:35:10 INFO::Fitting model to feature number 109, PWY.1861..formaldehyde.assimilation.II..RuMP.Cycle.
## 2021-07-28 09:35:10 INFO::Fitting model to feature number 110, PWY.241..C4.photosynthetic.carbon.assimilation.cycle..NADP.ME.type
## 2021-07-28 09:35:10 INFO::Fitting model to feature number 111, PWY.2723..trehalose.degradation.V
## 2021-07-28 09:35:10 INFO::Fitting model to feature number 112, PWY.2941..L.lysine.biosynthesis.II
## 2021-07-28 09:35:10 INFO::Fitting model to feature number 113, PWY.2942..L.lysine.biosynthesis.III## boundary (singular) fit: see ?isSingular## 2021-07-28 09:35:10 INFO::Fitting model to feature number 114, PWY.3001..superpathway.of.L.isoleucine.biosynthesis.I## boundary (singular) fit: see ?isSingular## 2021-07-28 09:35:10 INFO::Fitting model to feature number 115, PWY.3781..aerobic.respiration.I..cytochrome.c.
## 2021-07-28 09:35:10 INFO::Fitting model to feature number 116, PWY.3841..folate.transformations.II
## 2021-07-28 09:35:10 INFO::Fitting model to feature number 117, PWY.4041...gamma..glutamyl.cycle
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 118, PWY.4242..pantothenate.and.coenzyme.A.biosynthesis.III
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 119, PWY.4361..S.methyl.5.thio..alpha..D.ribose.1.phosphate.degradation
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 120, PWY.4702..phytate.degradation.I
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 121, PWY.4981..L.proline.biosynthesis.II..from.arginine.
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 122, PWY.4984..urea.cycle
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 123, PWY.5005..biotin.biosynthesis.II
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 124, PWY.5022..4.aminobutanoate.degradation.V
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 125, PWY.5030..L.histidine.degradation.III
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 126, PWY.5083..NAD.NADH.phosphorylation.and.dephosphorylation
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 127, PWY.5097..L.lysine.biosynthesis.VI## boundary (singular) fit: see ?isSingular## 2021-07-28 09:35:11 INFO::Fitting model to feature number 128, PWY.5100..pyruvate.fermentation.to.acetate.and.lactate.II
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 129, PWY.5101..L.isoleucine.biosynthesis.II
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 130, PWY.5103..L.isoleucine.biosynthesis.III
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 131, PWY.5104..L.isoleucine.biosynthesis.IV
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 132, PWY.5121..superpathway.of.geranylgeranyl.diphosphate.biosynthesis.II..via.MEP.
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 133, PWY.5136..fatty.acid..beta..oxidation.II..peroxisome.
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 134, PWY.5138..unsaturated..even.numbered.fatty.acid..beta..oxidation
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 135, PWY.5154..L.arginine.biosynthesis.III..via.N.acetyl.L.citrulline.
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 136, PWY.5173..superpathway.of.acetyl.CoA.biosynthesis
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 137, PWY.5177..glutaryl.CoA.degradation
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 138, PWY.5188..tetrapyrrole.biosynthesis.I..from.glutamate.
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 139, PWY.5189..tetrapyrrole.biosynthesis.II..from.glycine.
## 2021-07-28 09:35:11 INFO::Fitting model to feature number 140, PWY.5265..peptidoglycan.biosynthesis.II..staphylococci.
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 141, PWY.5304..superpathway.of.sulfur.oxidation..Acidianus.ambivalens.
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 142, PWY.5345..superpathway.of.L.methionine.biosynthesis..by.sulfhydrylation.
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 143, PWY.5347..superpathway.of.L.methionine.biosynthesis..transsulfuration.
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 144, PWY.5367..petroselinate.biosynthesis
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 145, PWY.5384..sucrose.degradation.IV..sucrose.phosphorylase.
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 146, PWY.5415..catechol.degradation.I..meta.cleavage.pathway.
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 147, PWY.5464..superpathway.of.cytosolic.glycolysis..plants...pyruvate.dehydrogenase.and.TCA.cycle
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 148, PWY.5484..glycolysis.II..from.fructose.6.phosphate.
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 149, PWY.5505..L.glutamate.and.L.glutamine.biosynthesis
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 150, PWY.561..superpathway.of.glyoxylate.cycle.and.fatty.acid.degradation
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 151, PWY.5656..mannosylglycerate.biosynthesis.I
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 152, PWY.5659..GDP.mannose.biosynthesis
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 153, PWY.5667..CDP.diacylglycerol.biosynthesis.I
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 154, PWY.5675..nitrate.reduction.V..assimilatory.
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 155, PWY.5676..acetyl.CoA.fermentation.to.butanoate.II
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 156, PWY.5686..UMP.biosynthesis
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 157, PWY.5690..TCA.cycle.II..plants.and.fungi.
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 158, PWY.5695..urate.biosynthesis.inosine.5..phosphate.degradation
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 159, PWY.5705..allantoin.degradation.to.glyoxylate.III
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 160, PWY.5723..Rubisco.shunt
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 161, PWY.5747..2.methylcitrate.cycle.II
## 2021-07-28 09:35:12 INFO::Fitting model to feature number 162, PWY.5791..1.4.dihydroxy.2.naphthoate.biosynthesis.II..plants.
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 163, PWY.5837..1.4.dihydroxy.2.naphthoate.biosynthesis.I
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 164, PWY.5838..superpathway.of.menaquinol.8.biosynthesis.I
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 165, PWY.5840..superpathway.of.menaquinol.7.biosynthesis
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 166, PWY.5845..superpathway.of.menaquinol.9.biosynthesis
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 167, PWY.5850..superpathway.of.menaquinol.6.biosynthesis.I
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 168, PWY.5855..ubiquinol.7.biosynthesis..prokaryotic.
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 169, PWY.5856..ubiquinol.9.biosynthesis..prokaryotic.
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 170, PWY.5857..ubiquinol.10.biosynthesis..prokaryotic.
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 171, PWY.5860..superpathway.of.demethylmenaquinol.6.biosynthesis.I
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 172, PWY.5861..superpathway.of.demethylmenaquinol.8.biosynthesis
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 173, PWY.5862..superpathway.of.demethylmenaquinol.9.biosynthesis
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 174, PWY.5863..superpathway.of.phylloquinol.biosynthesis
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 175, PWY.5896..superpathway.of.menaquinol.10.biosynthesis
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 176, PWY.5897..superpathway.of.menaquinol.11.biosynthesis
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 177, PWY.5898..superpathway.of.menaquinol.12.biosynthesis
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 178, PWY.5899..superpathway.of.menaquinol.13.biosynthesis
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 179, PWY.5910..superpathway.of.geranylgeranyldiphosphate.biosynthesis.I..via.mevalonate.
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 180, PWY.5913..TCA.cycle.VI..obligate.autotrophs.
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 181, PWY.5918..superpathay.of.heme.biosynthesis.from.glutamate
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 182, PWY.5920..superpathway.of.heme.biosynthesis.from.glycine
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 183, PWY.5941..glycogen.degradation.II..eukaryotic.
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 184, PWY.5971..palmitate.biosynthesis.II..bacteria.and.plants.
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 185, PWY.5973..cis.vaccenate.biosynthesis
## 2021-07-28 09:35:13 INFO::Fitting model to feature number 186, PWY.5989..stearate.biosynthesis.II..bacteria.and.plants.
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 187, PWY.6113..superpathway.of.mycolate.biosynthesis
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 188, PWY.6121..5.aminoimidazole.ribonucleotide.biosynthesis.I
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 189, PWY.6122..5.aminoimidazole.ribonucleotide.biosynthesis.II
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 190, PWY.6123..inosine.5..phosphate.biosynthesis.I
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 191, PWY.6124..inosine.5..phosphate.biosynthesis.II
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 192, PWY.6125..superpathway.of.guanosine.nucleotides.de.novo.biosynthesis.II
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 193, PWY.6126..superpathway.of.adenosine.nucleotides.de.novo.biosynthesis.II
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 194, PWY.6147..6.hydroxymethyl.dihydropterin.diphosphate.biosynthesis.I
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 195, PWY.6151..S.adenosyl.L.methionine.cycle.I
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 196, PWY.6163..chorismate.biosynthesis.from.3.dehydroquinate
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 197, PWY.6168..flavin.biosynthesis.III..fungi.
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 198, PWY.621..sucrose.degradation.III..sucrose.invertase.
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 199, PWY.6270..isoprene.biosynthesis.I
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 200, PWY.6277..superpathway.of.5.aminoimidazole.ribonucleotide.biosynthesis
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 201, PWY.6282..palmitoleate.biosynthesis.I..from..5Z..dodec.5.enoate.
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 202, PWY.6284..superpathway.of.unsaturated.fatty.acids.biosynthesis..E..coli.
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 203, PWY.6285..superpathway.of.fatty.acids.biosynthesis..E..coli.
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 204, PWY.6305..putrescine.biosynthesis.IV
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 205, PWY.6317..galactose.degradation.I..Leloir.pathway.
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 206, PWY.6353..purine.nucleotides.degradation.II..aerobic.
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 207, PWY.6385..peptidoglycan.biosynthesis.III..mycobacteria.
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 208, PWY.6386..UDP.N.acetylmuramoyl.pentapeptide.biosynthesis.II..lysine.containing.
## 2021-07-28 09:35:14 INFO::Fitting model to feature number 209, PWY.6387..UDP.N.acetylmuramoyl.pentapeptide.biosynthesis.I..meso.diaminopimelate.containing.## boundary (singular) fit: see ?isSingular## 2021-07-28 09:35:15 INFO::Fitting model to feature number 210, PWY.6396..superpathway.of.2.3.butanediol.biosynthesis
## 2021-07-28 09:35:15 INFO::Fitting model to feature number 211, PWY.6467..Kdo.transfer.to.lipid.IVA.III..Chlamydia.
## 2021-07-28 09:35:15 INFO::Fitting model to feature number 212, PWY.6471..peptidoglycan.biosynthesis.IV..Enterococcus.faecium.
## 2021-07-28 09:35:15 INFO::Fitting model to feature number 213, PWY.6507..4.deoxy.L.threo.hex.4.enopyranuronate.degradation
## 2021-07-28 09:35:15 INFO::Fitting model to feature number 214, PWY.6519..8.amino.7.oxononanoate.biosynthesis.I
## 2021-07-28 09:35:15 INFO::Fitting model to feature number 215, PWY.6527..stachyose.degradation
## 2021-07-28 09:35:15 INFO::Fitting model to feature number 216, PWY.6531..mannitol.cycle
## 2021-07-28 09:35:15 INFO::Fitting model to feature number 217, PWY.6545..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.III
## 2021-07-28 09:35:15 INFO::Fitting model to feature number 218, PWY.6549..L.glutamine.biosynthesis.III
## 2021-07-28 09:35:15 INFO::Fitting model to feature number 219, PWY.6588..pyruvate.fermentation.to.acetone
## 2021-07-28 09:35:15 INFO::Fitting model to feature number 220, PWY.6590..superpathway.of.Clostridium.acetobutylicum.acidogenic.fermentation
## 2021-07-28 09:35:15 INFO::Fitting model to feature number 221, PWY.6595..superpathway.of.guanosine.nucleotides.degradation..plants.
## 2021-07-28 09:35:15 INFO::Fitting model to feature number 222, PWY.6606..guanosine.nucleotides.degradation.II
## 2021-07-28 09:35:15 INFO::Fitting model to feature number 223, PWY.6608..guanosine.nucleotides.degradation.III
## 2021-07-28 09:35:15 INFO::Fitting model to feature number 224, PWY.6609..adenine.and.adenosine.salvage.III
## 2021-07-28 09:35:15 INFO::Fitting model to feature number 225, PWY.6612..superpathway.of.tetrahydrofolate.biosynthesis
## 2021-07-28 09:35:15 INFO::Fitting model to feature number 226, PWY.6628..superpathway.of.L.phenylalanine.biosynthesis
## 2021-07-28 09:35:15 INFO::Fitting model to feature number 227, PWY.6629..superpathway.of.L.tryptophan.biosynthesis
## 2021-07-28 09:35:15 INFO::Fitting model to feature number 228, PWY.6630..superpathway.of.L.tyrosine.biosynthesis
## 2021-07-28 09:35:15 INFO::Fitting model to feature number 229, PWY.6690..cinnamate.and.3.hydroxycinnamate.degradation.to.2.oxopent.4.enoate
## 2021-07-28 09:35:15 INFO::Fitting model to feature number 230, PWY.6700..queuosine.biosynthesis
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 231, PWY.6703..preQ0.biosynthesis
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 232, PWY.6708..ubiquinol.8.biosynthesis..prokaryotic.
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 233, PWY.6731..starch.degradation.III
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 234, PWY.6737..starch.degradation.V
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 235, PWY.6803..phosphatidylcholine.acyl.editing
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 236, PWY.6823..molybdenum.cofactor.biosynthesis
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 237, PWY.6859..all.trans.farnesol.biosynthesis
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 238, PWY.6891..thiazole.biosynthesis.II..Bacillus.
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 239, PWY.6892..thiazole.biosynthesis.I..E..coli.
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 240, PWY.6895..superpathway.of.thiamin.diphosphate.biosynthesis.II
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 241, PWY.6897..thiamin.salvage.II
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 242, PWY.6901..superpathway.of.glucose.and.xylose.degradation
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 243, PWY.6936..seleno.amino.acid.biosynthesis
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 244, PWY.6969..TCA.cycle.V..2.oxoglutarate.ferredoxin.oxidoreductase.
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 245, PWY.7003..glycerol.degradation.to.butanol
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 246, PWY.7013..L.1.2.propanediol.degradation
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 247, PWY.7039..phosphatidate.metabolism..as.a.signaling.molecule
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 248, PWY.7111..pyruvate.fermentation.to.isobutanol..engineered.
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 249, PWY.7115..C4.photosynthetic.carbon.assimilation.cycle..NAD.ME.type
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 250, PWY.7117..C4.photosynthetic.carbon.assimilation.cycle..PEPCK.type
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 251, PWY.7184..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.I
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 252, PWY.7187..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.II
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 253, PWY.7196..superpathway.of.pyrimidine.ribonucleosides.salvage
## 2021-07-28 09:35:16 INFO::Fitting model to feature number 254, PWY.7197..pyrimidine.deoxyribonucleotide.phosphorylation
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 255, PWY.7198..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.IV
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 256, PWY.7199..pyrimidine.deoxyribonucleosides.salvage
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 257, PWY.7204..pyridoxal.5..phosphate.salvage.II..plants.
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 258, PWY.7208..superpathway.of.pyrimidine.nucleobases.salvage
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 259, PWY.7209..superpathway.of.pyrimidine.ribonucleosides.degradation
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 260, PWY.7210..pyrimidine.deoxyribonucleotides.biosynthesis.from.CTP
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 261, PWY.7211..superpathway.of.pyrimidine.deoxyribonucleotides.de.novo.biosynthesis
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 262, PWY.7219..adenosine.ribonucleotides.de.novo.biosynthesis
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 263, PWY.7220..adenosine.deoxyribonucleotides.de.novo.biosynthesis.II
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 264, PWY.7221..guanosine.ribonucleotides.de.novo.biosynthesis
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 265, PWY.7222..guanosine.deoxyribonucleotides.de.novo.biosynthesis.II
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 266, PWY.7228..superpathway.of.guanosine.nucleotides.de.novo.biosynthesis.I
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 267, PWY.7229..superpathway.of.adenosine.nucleotides.de.novo.biosynthesis.I
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 268, PWY.7234..inosine.5..phosphate.biosynthesis.III
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 269, PWY.7237..myo...chiro..and.scillo.inositol.degradation
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 270, PWY.7242..D.fructuronate.degradation
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 271, PWY.724..superpathway.of.L.lysine..L.threonine.and.L.methionine.biosynthesis.II## boundary (singular) fit: see ?isSingular## 2021-07-28 09:35:17 INFO::Fitting model to feature number 272, PWY.7254..TCA.cycle.VII..acetate.producers.
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 273, PWY.7269..NAD.NADP.NADH.NADPH.mitochondrial.interconversion..yeast.
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 274, PWY.7279..aerobic.respiration.II..cytochrome.c...yeast.
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 275, PWY.7282..4.amino.2.methyl.5.phosphomethylpyrimidine.biosynthesis..yeast.
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 276, PWY.7315..dTDP.N.acetylthomosamine.biosynthesis
## 2021-07-28 09:35:17 INFO::Fitting model to feature number 277, PWY.7323..superpathway.of.GDP.mannose.derived.O.antigen.building.blocks.biosynthesis
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 278, PWY.7328..superpathway.of.UDP.glucose.derived.O.antigen.building.blocks.biosynthesis
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 279, PWY.7357..thiamin.formation.from.pyrithiamine.and.oxythiamine..yeast.
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 280, PWY.7383..anaerobic.energy.metabolism..invertebrates..cytosol.
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 281, PWY.7388..octanoyl..acyl.carrier.protein..biosynthesis..mitochondria..yeast.
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 282, PWY.7392..taxadiene.biosynthesis..engineered.
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 283, PWY.7399..methylphosphonate.degradation.II
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 284, PWY.7400..L.arginine.biosynthesis.IV..archaebacteria.
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 285, PWY.7409..phospholipid.remodeling..phosphatidylethanolamine..yeast.
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 286, PWY.7446..sulfoglycolysis
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 287, PWY.7456..mannan.degradation
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 288, PWY.7527..L.methionine.salvage.cycle.III
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 289, PWY.7539..6.hydroxymethyl.dihydropterin.diphosphate.biosynthesis.III..Chlamydia.
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 290, PWY.7560..methylerythritol.phosphate.pathway.II
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 291, PWY.7663..gondoate.biosynthesis..anaerobic.
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 292, PWY.7664..oleate.biosynthesis.IV..anaerobic.
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 293, PWY.821..superpathway.of.sulfur.amino.acid.biosynthesis..Saccharomyces.cerevisiae.
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 294, PWY.841..superpathway.of.purine.nucleotides.de.novo.biosynthesis.I
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 295, PWY.922..mevalonate.pathway.I
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 296, PWY0.1061..superpathway.of.L.alanine.biosynthesis
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 297, PWY0.1241..ADP.L.glycero..beta..D.manno.heptose.biosynthesis
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 298, PWY0.1261..anhydromuropeptides.recycling
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 299, PWY0.1277..3.phenylpropanoate.and.3..3.hydroxyphenyl.propanoate.degradation
## 2021-07-28 09:35:18 INFO::Fitting model to feature number 300, PWY0.1296..purine.ribonucleosides.degradation
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 301, PWY0.1297..superpathway.of.purine.deoxyribonucleosides.degradation## boundary (singular) fit: see ?isSingular## 2021-07-28 09:35:19 INFO::Fitting model to feature number 302, PWY0.1298..superpathway.of.pyrimidine.deoxyribonucleosides.degradation
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 303, PWY0.1319..CDP.diacylglycerol.biosynthesis.II
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 304, PWY0.1338..polymyxin.resistance
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 305, PWY0.1415..superpathway.of.heme.biosynthesis.from.uroporphyrinogen.III
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 306, PWY0.1479..tRNA.processing
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 307, PWY0.1533..methylphosphonate.degradation.I
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 308, PWY0.1586..peptidoglycan.maturation..meso.diaminopimelate.containing.
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 309, PWY0.162..superpathway.of.pyrimidine.ribonucleotides.de.novo.biosynthesis
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 310, PWY0.166..superpathway.of.pyrimidine.deoxyribonucleotides.de.novo.biosynthesis..E..coli.
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 311, PWY0.321..phenylacetate.degradation.I..aerobic.
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 312, PWY0.41..allantoin.degradation.IV..anaerobic.
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 313, PWY0.42..2.methylcitrate.cycle.I
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 314, PWY0.781..aspartate.superpathway
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 315, PWY0.845..superpathway.of.pyridoxal.5..phosphate.biosynthesis.and.salvage
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 316, PWY0.862...5Z..dodec.5.enoate.biosynthesis
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 317, PWY490.3..nitrate.reduction.VI..assimilatory.
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 318, PWY4FS.7..phosphatidylglycerol.biosynthesis.I..plastidic.
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 319, PWY4FS.8..phosphatidylglycerol.biosynthesis.II..non.plastidic.
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 320, PWY4LZ.257..superpathway.of.fermentation..Chlamydomonas.reinhardtii.
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 321, PWY66.389..phytol.degradation
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 322, PWY66.398..TCA.cycle.III..animals.
## 2021-07-28 09:35:19 INFO::Fitting model to feature number 323, PWY66.399..gluconeogenesis.III
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 324, PWY66.400..glycolysis.VI..metazoan.
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 325, PWY66.409..superpathway.of.purine.nucleotide.salvage
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 326, PWY66.422..D.galactose.degradation.V..Leloir.pathway.
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 327, PWYG.321..mycolate.biosynthesis
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 328, PYRIDNUCSAL.PWY..NAD.salvage.pathway.I
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 329, PYRIDNUCSYN.PWY..NAD.biosynthesis.I..from.aspartate.
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 330, PYRIDOXSYN.PWY..pyridoxal.5..phosphate.biosynthesis.I
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 331, REDCITCYC..TCA.cycle.VIII..helicobacter.
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 332, RHAMCAT.PWY..L.rhamnose.degradation.I
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 333, RIBOSYN2.PWY..flavin.biosynthesis.I..bacteria.and.plants.
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 334, SALVADEHYPOX.PWY..adenosine.nucleotides.degradation.II
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 335, SER.GLYSYN.PWY..superpathway.of.L.serine.and.glycine.biosynthesis.I
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 336, SO4ASSIM.PWY..sulfate.reduction.I..assimilatory.
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 337, SULFATE.CYS.PWY..superpathway.of.sulfate.assimilation.and.cysteine.biosynthesis
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 338, TCA.GLYOX.BYPASS..superpathway.of.glyoxylate.bypass.and.TCA
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 339, TCA..TCA.cycle.I..prokaryotic.
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 340, THISYN.PWY..superpathway.of.thiamin.diphosphate.biosynthesis.I
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 341, THISYNARA.PWY..superpathway.of.thiamin.diphosphate.biosynthesis.III..eukaryotes.
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 342, THRESYN.PWY..superpathway.of.L.threonine.biosynthesis
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 343, TRNA.CHARGING.PWY..tRNA.charging
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 344, TRPSYN.PWY..L.tryptophan.biosynthesis
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 345, UBISYN.PWY..superpathway.of.ubiquinol.8.biosynthesis..prokaryotic.
## 2021-07-28 09:35:20 INFO::Fitting model to feature number 346, UDPNAGSYN.PWY..UDP.N.acetyl.D.glucosamine.biosynthesis.I## boundary (singular) fit: see ?isSingular## 2021-07-28 09:35:20 INFO::Fitting model to feature number 347, VALSYN.PWY..L.valine.biosynthesis## boundary (singular) fit: see ?isSingular## 2021-07-28 09:35:21 INFO::Counting total values for each feature
## 2021-07-28 09:35:21 WARNING::Deleting existing residuals file: outputs/maaslin_functional/residuals.rds
## 2021-07-28 09:35:21 INFO::Writing residuals to file outputs/maaslin_functional/residuals.rds
## 2021-07-28 09:35:21 INFO::Writing all results to file (ordered by increasing q-values): outputs/maaslin_functional/all_results.tsv
## 2021-07-28 09:35:21 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): outputs/maaslin_functional/significant_results.tsv
## 2021-07-28 09:35:21 INFO::Writing heatmap of significant results to file: outputs/maaslin_functional/heatmap.pdf## 2021-07-28 09:35:21 INFO::Writing association plots (one for each significant association) to output folder: outputs/maaslin_functional
## 2021-07-28 09:35:21 INFO::Plotting associations from most to least significant, grouped by metadata
## 2021-07-28 09:35:21 INFO::Plotting data for metadata number 1, Group
## 2021-07-28 09:35:21 INFO::Creating boxplot for categorical data, Group vs PWY.5304..superpathway.of.sulfur.oxidation..Acidianus.ambivalens.## 2021-07-28 09:35:21 INFO::Creating boxplot for categorical data, Group vs OANTIGEN.PWY..O.antigen.building.blocks.biosynthesis..E..coli.## 2021-07-28 09:35:21 INFO::Creating boxplot for categorical data, Group vs PWY.724..superpathway.of.L.lysine..L.threonine.and.L.methionine.biosynthesis.II## 2021-07-28 09:35:21 INFO::Creating boxplot for categorical data, Group vs PWY66.399..gluconeogenesis.III## 2021-07-28 09:35:21 INFO::Creating boxplot for categorical data, Group vs PWY.6737..starch.degradation.V## 2021-07-28 09:35:21 INFO::Creating boxplot for categorical data, Group vs PWY.5173..superpathway.of.acetyl.CoA.biosynthesis## 2021-07-28 09:35:22 INFO::Creating boxplot for categorical data, Group vs PWY0.1297..superpathway.of.purine.deoxyribonucleosides.degradation## 2021-07-28 09:35:22 INFO::Creating boxplot for categorical data, Group vs PWY.5177..glutaryl.CoA.degradation## 2021-07-28 09:35:22 INFO::Creating boxplot for categorical data, Group vs PWY.5101..L.isoleucine.biosynthesis.II## 2021-07-28 09:35:22 INFO::Creating boxplot for categorical data, Group vs PWY.7003..glycerol.degradation.to.butanol## 2021-07-28 09:35:22 INFO::Creating boxplot for categorical data, Group vs PWY.5030..L.histidine.degradation.III## 2021-07-28 09:35:22 INFO::Creating boxplot for categorical data, Group vs PWY.7383..anaerobic.energy.metabolism..invertebrates..cytosol.## 2021-07-28 09:35:22 INFO::Creating boxplot for categorical data, Group vs NONMEVIPP.PWY..methylerythritol.phosphate.pathway.I## 2021-07-28 09:35:22 INFO::Creating boxplot for categorical data, Group vs PWY.2942..L.lysine.biosynthesis.III## 2021-07-28 09:35:22 INFO::Creating boxplot for categorical data, Group vs UNINTEGRATED## 2021-07-28 09:35:22 INFO::Creating boxplot for categorical data, Group vs DTDPRHAMSYN.PWY..dTDP.L.rhamnose.biosynthesis.I## 2021-07-28 09:35:23 INFO::Creating boxplot for categorical data, Group vs PWY.5304..superpathway.of.sulfur.oxidation..Acidianus.ambivalens.## 2021-07-28 09:35:23 INFO::Creating boxplot for categorical data, Group vs PWY66.389..phytol.degradation## 2021-07-28 09:35:23 INFO::Creating boxplot for categorical data, Group vs TRNA.CHARGING.PWY..tRNA.charging## 2021-07-28 09:35:23 INFO::Creating boxplot for categorical data, Group vs PWY.6151..S.adenosyl.L.methionine.cycle.I## 2021-07-28 09:35:23 INFO::Creating boxplot for categorical data, Group vs PWY.5097..L.lysine.biosynthesis.VI## 2021-07-28 09:35:23 INFO::Creating boxplot for categorical data, Group vs PWY.7196..superpathway.of.pyrimidine.ribonucleosides.salvage## 2021-07-28 09:35:23 INFO::Creating boxplot for categorical data, Group vs PWY.7456..mannan.degradation## 2021-07-28 09:35:23 INFO::Creating boxplot for categorical data, Group vs ILEUSYN.PWY..L.isoleucine.biosynthesis.I..from.threonine.## 2021-07-28 09:35:23 INFO::Creating boxplot for categorical data, Group vs ARO.PWY..chorismate.biosynthesis.I## 2021-07-28 09:35:23 INFO::Creating boxplot for categorical data, Group vs COMPLETE.ARO.PWY..superpathway.of.aromatic.amino.acid.biosynthesis## 2021-07-28 09:35:24 INFO::Creating boxplot for categorical data, Group vs P125.PWY..superpathway.of..R.R..butanediol.biosynthesis## 2021-07-28 09:35:24 INFO::Creating boxplot for categorical data, Group vs VALSYN.PWY..L.valine.biosynthesis## 2021-07-28 09:35:24 INFO::Creating boxplot for categorical data, Group vs PWY.5686..UMP.biosynthesis## 2021-07-28 09:35:24 INFO::Creating boxplot for categorical data, Group vs PWY0.862...5Z..dodec.5.enoate.biosynthesis## 2021-07-28 09:35:24 INFO::Creating boxplot for categorical data, Group vs PWY.6317..galactose.degradation.I..Leloir.pathway.## 2021-07-28 09:35:24 INFO::Creating boxplot for categorical data, Group vs PWY.6588..pyruvate.fermentation.to.acetone## 2021-07-28 09:35:24 INFO::Creating boxplot for categorical data, Group vs PWYG.321..mycolate.biosynthesis## 2021-07-28 09:35:24 INFO::Creating boxplot for categorical data, Group vs PWY.1861..formaldehyde.assimilation.II..RuMP.Cycle.## 2021-07-28 09:35:24 INFO::Creating boxplot for categorical data, Group vs UNMAPPED## 2021-07-28 09:35:24 INFO::Creating boxplot for categorical data, Group vs P562.PWY..myo.inositol.degradation.I## 2021-07-28 09:35:25 INFO::Creating boxplot for categorical data, Group vs HISTSYN.PWY..L.histidine.biosynthesis## 2021-07-28 09:35:25 INFO::Creating boxplot for categorical data, Group vs PWY.6549..L.glutamine.biosynthesis.III## 2021-07-28 09:35:25 INFO::Creating boxplot for categorical data, Group vs PWY0.1319..CDP.diacylglycerol.biosynthesis.II## 2021-07-28 09:35:25 INFO::Creating boxplot for categorical data, Group vs PWY490.3..nitrate.reduction.VI..assimilatory.## 2021-07-28 09:35:25 INFO::Creating boxplot for categorical data, Group vs SO4ASSIM.PWY..sulfate.reduction.I..assimilatory.## 2021-07-28 09:35:25 INFO::Creating boxplot for categorical data, Group vs PWY.5973..cis.vaccenate.biosynthesis## 2021-07-28 09:35:25 INFO::Creating boxplot for categorical data, Group vs POLYAMINSYN3.PWY..superpathway.of.polyamine.biosynthesis.II## 2021-07-28 09:35:25 INFO::Creating boxplot for categorical data, Group vs PWY.3001..superpathway.of.L.isoleucine.biosynthesis.I## 2021-07-28 09:35:25 INFO::Creating boxplot for categorical data, Group vs PRPP.PWY..superpathway.of.histidine..purine..and.pyrimidine.biosynthesis## 2021-07-28 09:35:25 INFO::Creating boxplot for categorical data, Group vs P185.PWY..formaldehyde.assimilation.III..dihydroxyacetone.cycle.## 2021-07-28 09:35:26 INFO::Creating boxplot for categorical data, Group vs PWY.5505..L.glutamate.and.L.glutamine.biosynthesis## 2021-07-28 09:35:26 INFO::Creating boxplot for categorical data, Group vs PWY.5667..CDP.diacylglycerol.biosynthesis.I## 2021-07-28 09:35:26 INFO::Creating boxplot for categorical data, Group vs PWY66.422..D.galactose.degradation.V..Leloir.pathway.## 2021-07-28 09:35:26 INFO::Creating boxplot for categorical data, Group vs PWY.6163..chorismate.biosynthesis.from.3.dehydroquinate## 2021-07-28 09:35:26 INFO::Creating boxplot for categorical data, Group vs PEPTIDOGLYCANSYN.PWY..peptidoglycan.biosynthesis.I..meso.diaminopimelate.containing.## 2021-07-28 09:35:26 INFO::Creating boxplot for categorical data, Group vs PWY.621..sucrose.degradation.III..sucrose.invertase.## 2021-07-28 09:35:26 INFO::Creating boxplot for categorical data, Group vs PWY.6387..UDP.N.acetylmuramoyl.pentapeptide.biosynthesis.I..meso.diaminopimelate.containing.## 2021-07-28 09:35:26 INFO::Creating boxplot for categorical data, Group vs BRANCHED.CHAIN.AA.SYN.PWY..superpathway.of.branched.amino.acid.biosynthesis## 2021-07-28 09:35:26 INFO::Creating boxplot for categorical data, Group vs PWY.7209..superpathway.of.pyrimidine.ribonucleosides.degradation## 2021-07-28 09:35:27 INFO::Creating boxplot for categorical data, Group vs PWY.4984..urea.cycle## 2021-07-28 09:35:27 INFO::Creating boxplot for categorical data, Group vs PWY.5101..L.isoleucine.biosynthesis.II## 2021-07-28 09:35:27 INFO::Creating boxplot for categorical data, Group vs PWY.7111..pyruvate.fermentation.to.isobutanol..engineered.## 2021-07-28 09:35:27 INFO::Creating boxplot for categorical data, Group vs PWY.7456..mannan.degradation## 2021-07-28 09:35:27 INFO::Creating boxplot for categorical data, Group vs PWY.6527..stachyose.degradation## 2021-07-28 09:35:27 INFO::Creating boxplot for categorical data, Group vs PWY.5265..peptidoglycan.biosynthesis.II..staphylococci.## 2021-07-28 09:35:27 INFO::Creating boxplot for categorical data, Group vs GALACT.GLUCUROCAT.PWY..superpathway.of.hexuronide.and.hexuronate.degradation## 2021-07-28 09:35:27 INFO::Creating boxplot for categorical data, Group vs GLUCUROCAT.PWY..superpathway.of..beta..D.glucuronide.and.D.glucuronate.degradation## 2021-07-28 09:35:27 INFO::Creating boxplot for categorical data, Group vs HEME.BIOSYNTHESIS.II..heme.biosynthesis.I..aerobic.## 2021-07-28 09:35:28 INFO::Creating boxplot for categorical data, Group vs PWY.7003..glycerol.degradation.to.butanol## 2021-07-28 09:35:28 INFO::Creating boxplot for categorical data, Group vs PWY.5910..superpathway.of.geranylgeranyldiphosphate.biosynthesis.I..via.mevalonate.## 2021-07-28 09:35:28 INFO::Creating boxplot for categorical data, Group vs PWY.6113..superpathway.of.mycolate.biosynthesis## 2021-07-28 09:35:28 INFO::Creating boxplot for categorical data, Group vs PWY.6545..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.III## 2021-07-28 09:35:28 INFO::Creating boxplot for categorical data, Group vs PWY.7392..taxadiene.biosynthesis..engineered.## 2021-07-28 09:35:28 INFO::Creating boxplot for categorical data, Group vs PWY.5265..peptidoglycan.biosynthesis.II..staphylococci.## 2021-07-28 09:35:28 INFO::Creating boxplot for categorical data, Group vs SER.GLYSYN.PWY..superpathway.of.L.serine.and.glycine.biosynthesis.I## 2021-07-28 09:35:28 INFO::Creating boxplot for categorical data, Group vs COBALSYN.PWY..adenosylcobalamin.salvage.from.cobinamide.I## 2021-07-28 09:35:28 INFO::Creating boxplot for categorical data, Group vs PWY.5676..acetyl.CoA.fermentation.to.butanoate.II## 2021-07-28 09:35:28 INFO::Creating boxplot for categorical data, Group vs PWY.5103..L.isoleucine.biosynthesis.III## 2021-07-28 09:35:29 INFO::Creating boxplot for categorical data, Group vs PWY.7400..L.arginine.biosynthesis.IV..archaebacteria.## 2021-07-28 09:35:29 INFO::Creating boxplot for categorical data, Group vs HSERMETANA.PWY..L.methionine.biosynthesis.III## 2021-07-28 09:35:29 INFO::Creating boxplot for categorical data, Group vs THISYNARA.PWY..superpathway.of.thiamin.diphosphate.biosynthesis.III..eukaryotes.## 2021-07-28 09:35:29 INFO::Creating boxplot for categorical data, Group vs PWY.6595..superpathway.of.guanosine.nucleotides.degradation..plants.## 2021-07-28 09:35:29 INFO::Creating boxplot for categorical data, Group vs GALACT.GLUCUROCAT.PWY..superpathway.of.hexuronide.and.hexuronate.degradation## 2021-07-28 09:35:29 INFO::Creating boxplot for categorical data, Group vs PANTOSYN.PWY..pantothenate.and.coenzyme.A.biosynthesis.I## 2021-07-28 09:35:29 INFO::Creating boxplot for categorical data, Group vs POLYAMINSYN3.PWY..superpathway.of.polyamine.biosynthesis.II## 2021-07-28 09:35:29 INFO::Creating boxplot for categorical data, Group vs PYRIDNUCSYN.PWY..NAD.biosynthesis.I..from.aspartate.## 2021-07-28 09:35:30 INFO::Creating boxplot for categorical data, Group vs PWY.5855..ubiquinol.7.biosynthesis..prokaryotic.## 2021-07-28 09:35:30 INFO::Creating boxplot for categorical data, Group vs PWY.5856..ubiquinol.9.biosynthesis..prokaryotic.## 2021-07-28 09:35:30 INFO::Creating boxplot for categorical data, Group vs PWY.5857..ubiquinol.10.biosynthesis..prokaryotic.## 2021-07-28 09:35:30 INFO::Creating boxplot for categorical data, Group vs PWY.6708..ubiquinol.8.biosynthesis..prokaryotic.## 2021-07-28 09:35:30 INFO::Creating boxplot for categorical data, Group vs PWY490.3..nitrate.reduction.VI..assimilatory.## 2021-07-28 09:35:30 INFO::Creating boxplot for categorical data, Group vs GLUDEG.I.PWY..GABA.shunt## 2021-07-28 09:35:30 INFO::Creating boxplot for categorical data, Group vs PWY.6531..mannitol.cycle## 2021-07-28 09:35:30 INFO::Creating boxplot for categorical data, Group vs GLUCUROCAT.PWY..superpathway.of..beta..D.glucuronide.and.D.glucuronate.degradation## 2021-07-28 09:35:30 INFO::Creating boxplot for categorical data, Group vs PWY.6396..superpathway.of.2.3.butanediol.biosynthesis## 2021-07-28 09:35:31 INFO::Creating boxplot for categorical data, Group vs ANAGLYCOLYSIS.PWY..glycolysis.III..from.glucose.## 2021-07-28 09:35:31 INFO::Creating boxplot for categorical data, Group vs PWY.1861..formaldehyde.assimilation.II..RuMP.Cycle.## 2021-07-28 09:35:31 INFO::Creating boxplot for categorical data, Group vs CALVIN.PWY..Calvin.Benson.Bassham.cycle## 2021-07-28 09:35:31 INFO::Creating boxplot for categorical data, Group vs COA.PWY..coenzyme.A.biosynthesis.I## 2021-07-28 09:35:31 INFO::Creating boxplot for categorical data, Group vs GALACTUROCAT.PWY..D.galacturonate.degradation.I## 2021-07-28 09:35:31 INFO::Creating boxplot for categorical data, Group vs TRPSYN.PWY..L.tryptophan.biosynthesis## 2021-07-28 09:35:31 INFO::Creating boxplot for categorical data, Group vs PWY.6609..adenine.and.adenosine.salvage.III## 2021-07-28 09:35:31 INFO::Creating boxplot for categorical data, Group vs P42.PWY..incomplete.reductive.TCA.cycle## 2021-07-28 09:35:31 INFO::Creating boxplot for categorical data, Group vs ARGSYNBSUB.PWY..L.arginine.biosynthesis.II..acetyl.cycle.## 2021-07-28 09:35:32 INFO::Creating boxplot for categorical data, Group vs NONOXIPENT.PWY..pentose.phosphate.pathway..non.oxidative.branch.## 2021-07-28 09:35:32 INFO::Creating boxplot for categorical data, Group vs PWY.5083..NAD.NADH.phosphorylation.and.dephosphorylation## 2021-07-28 09:35:32 INFO::Creating boxplot for categorical data, Group vs PWY.6897..thiamin.salvage.II## 2021-07-28 09:35:32 INFO::Creating boxplot for categorical data, Group vs ARGSYN.PWY..L.arginine.biosynthesis.I..via.L.ornithine.## 2021-07-28 09:35:32 INFO::Creating boxplot for categorical data, Group vs PWY.5173..superpathway.of.acetyl.CoA.biosynthesis## 2021-07-28 09:35:32 INFO::Creating boxplot for categorical data, Group vs UDPNAGSYN.PWY..UDP.N.acetyl.D.glucosamine.biosynthesis.I## 2021-07-28 09:35:32 INFO::Creating boxplot for categorical data, Group vs GLYCOGENSYNTH.PWY..glycogen.biosynthesis.I..from.ADP.D.Glucose.## 2021-07-28 09:35:32 INFO::Creating boxplot for categorical data, Group vs HEMESYN2.PWY..heme.biosynthesis.II..anaerobic.## 2021-07-28 09:35:33 INFO::Creating boxplot for categorical data, Group vs ARGORNPROST.PWY..arginine..ornithine.and.proline.interconversion## 2021-07-28 09:35:33 INFO::Creating boxplot for categorical data, Group vs GLUCONEO.PWY..gluconeogenesis.I## 2021-07-28 09:35:33 INFO::Creating boxplot for categorical data, Group vs P162.PWY..L.glutamate.degradation.V..via.hydroxyglutarate.## 2021-07-28 09:35:33 INFO::Creating boxplot for categorical data, Group vs PWY.6703..preQ0.biosynthesis## 2021-07-28 09:35:33 INFO::Creating boxplot for categorical data, Group vs PWY.7211..superpathway.of.pyrimidine.deoxyribonucleotides.de.novo.biosynthesis## 2021-07-28 09:35:33 INFO::Creating boxplot for categorical data, Group vs PWY.7242..D.fructuronate.degradation## 2021-07-28 09:35:33 INFO::Creating boxplot for categorical data, Group vs PWY0.781..aspartate.superpathway## 2021-07-28 09:35:33 INFO::Creating boxplot for categorical data, Group vs PWY.922..mevalonate.pathway.I## 2021-07-28 09:35:33 INFO::Creating boxplot for categorical data, Group vs COA.PWY.1..coenzyme.A.biosynthesis.II..mammalian.## 2021-07-28 09:35:33 INFO::Creating boxplot for categorical data, Group vs PWY.5121..superpathway.of.geranylgeranyl.diphosphate.biosynthesis.II..via.MEP.## 2021-07-28 09:35:34 INFO::Creating boxplot for categorical data, Group vs PWY.5177..glutaryl.CoA.degradation## 2021-07-28 09:35:34 INFO::Creating boxplot for categorical data, Group vs PWY.3781..aerobic.respiration.I..cytochrome.c.## 2021-07-28 09:35:34 INFO::Creating boxplot for categorical data, Group vs GALACTUROCAT.PWY..D.galacturonate.degradation.I## 2021-07-28 09:35:34 INFO::Creating boxplot for categorical data, Group vs PRPP.PWY..superpathway.of.histidine..purine..and.pyrimidine.biosynthesis## 2021-07-28 09:35:34 INFO::Creating boxplot for categorical data, Group vs PWY.7198..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.IV## 2021-07-28 09:35:34 INFO::Creating boxplot for categorical data, Group vs PWY.7210..pyrimidine.deoxyribonucleotides.biosynthesis.from.CTP## 2021-07-28 09:35:34 INFO::Creating boxplot for categorical data, Group vs HEMESYN2.PWY..heme.biosynthesis.II..anaerobic.## 2021-07-28 09:35:34 INFO::Creating boxplot for categorical data, Group vs ANAEROFRUCAT.PWY..homolactic.fermentation## 2021-07-28 09:35:34 INFO::Creating boxplot for categorical data, Group vs P164.PWY..purine.nucleobases.degradation.I..anaerobic.## 2021-07-28 09:35:34 INFO::Creating boxplot for categorical data, Group vs PWY.5918..superpathay.of.heme.biosynthesis.from.glutamate## 2021-07-28 09:35:35 INFO::Creating boxplot for categorical data, Group vs PWY.6168..flavin.biosynthesis.III..fungi.## 2021-07-28 09:35:35 INFO::Creating boxplot for categorical data, Group vs P108.PWY..pyruvate.fermentation.to.propanoate.I## 2021-07-28 09:35:35 INFO::Creating boxplot for categorical data, Group vs PWY.1042..glycolysis.IV..plant.cytosol.## 2021-07-28 09:35:35 INFO::Creating boxplot for categorical data, Group vs PWY.6122..5.aminoimidazole.ribonucleotide.biosynthesis.II## 2021-07-28 09:35:35 INFO::Creating boxplot for categorical data, Group vs PWY.6277..superpathway.of.5.aminoimidazole.ribonucleotide.biosynthesis## 2021-07-28 09:35:35 INFO::Creating boxplot for categorical data, Group vs PWY.7242..D.fructuronate.degradation## 2021-07-28 09:35:35 INFO::Creating boxplot for categorical data, Group vs PWY0.1241..ADP.L.glycero..beta..D.manno.heptose.biosynthesis## 2021-07-28 09:35:35 INFO::Creating boxplot for categorical data, Group vs PYRIDNUCSYN.PWY..NAD.biosynthesis.I..from.aspartate.## 2021-07-28 09:35:35 INFO::Creating boxplot for categorical data, Group vs PWY.7187..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.II## 2021-07-28 09:35:35 INFO::Creating boxplot for categorical data, Group vs PWY0.862...5Z..dodec.5.enoate.biosynthesis## 2021-07-28 09:35:36 INFO::Creating boxplot for categorical data, Group vs PYRIDOXSYN.PWY..pyridoxal.5..phosphate.biosynthesis.I## 2021-07-28 09:35:36 INFO::Creating boxplot for categorical data, Group vs COLANSYN.PWY..colanic.acid.building.blocks.biosynthesis## 2021-07-28 09:35:36 INFO::Creating boxplot for categorical data, Group vs PWY.4981..L.proline.biosynthesis.II..from.arginine.## 2021-07-28 09:35:36 INFO::Creating boxplot for categorical data, Group vs PWY.6121..5.aminoimidazole.ribonucleotide.biosynthesis.I## 2021-07-28 09:35:36 INFO::Creating boxplot for categorical data, Group vs PWY.922..mevalonate.pathway.I## 2021-07-28 09:35:36 INFO::Creating boxplot for categorical data, Group vs PWY.7115..C4.photosynthetic.carbon.assimilation.cycle..NAD.ME.type## 2021-07-28 09:35:36 INFO::Creating boxplot for categorical data, Group vs PWY.6151..S.adenosyl.L.methionine.cycle.I## 2021-07-28 09:35:36 INFO::Creating boxplot for categorical data, Group vs PWY0.1261..anhydromuropeptides.recycling## 2021-07-28 09:35:36 INFO::Creating boxplot for categorical data, Group vs PWY66.389..phytol.degradation## 2021-07-28 09:35:36 INFO::Creating boxplot for categorical data, Group vs DENOVOPURINE2.PWY..superpathway.of.purine.nucleotides.de.novo.biosynthesis.II## 2021-07-28 09:35:37 INFO::Creating boxplot for categorical data, Group vs PWY.6113..superpathway.of.mycolate.biosynthesis## 2021-07-28 09:35:37 INFO::Creating boxplot for categorical data, Group vs PWY.5154..L.arginine.biosynthesis.III..via.N.acetyl.L.citrulline.## 2021-07-28 09:35:37 INFO::Creating boxplot for categorical data, Group vs OANTIGEN.PWY..O.antigen.building.blocks.biosynthesis..E..coli.## 2021-07-28 09:35:37 INFO::Creating boxplot for categorical data, Group vs PWY.7221..guanosine.ribonucleotides.de.novo.biosynthesis## 2021-07-28 09:35:37 INFO::Creating boxplot for categorical data, Group vs PWY.5659..GDP.mannose.biosynthesis## 2021-07-28 09:35:37 INFO::Creating boxplot for categorical data, Group vs PWY.7219..adenosine.ribonucleotides.de.novo.biosynthesis## 2021-07-28 09:35:37 INFO::Creating boxplot for categorical data, Group vs PWY0.845..superpathway.of.pyridoxal.5..phosphate.biosynthesis.and.salvage## 2021-07-28 09:35:37 INFO::Creating boxplot for categorical data, Group vs PYRIDOXSYN.PWY..pyridoxal.5..phosphate.biosynthesis.I## 2021-07-28 09:35:37 INFO::Creating boxplot for categorical data, Group vs PWY0.162..superpathway.of.pyrimidine.ribonucleotides.de.novo.biosynthesis## 2021-07-28 09:35:37 INFO::Creating boxplot for categorical data, Group vs PWY.7228..superpathway.of.guanosine.nucleotides.de.novo.biosynthesis.I## 2021-07-28 09:35:37 INFO::Creating boxplot for categorical data, Group vs PWY.6386..UDP.N.acetylmuramoyl.pentapeptide.biosynthesis.II..lysine.containing.## 2021-07-28 09:35:38 INFO::Creating boxplot for categorical data, Group vs P161.PWY..acetylene.degradation## 2021-07-28 09:35:38 INFO::Creating boxplot for categorical data, Group vs MET.SAM.PWY..superpathway.of.S.adenosyl.L.methionine.biosynthesis## 2021-07-28 09:35:38 INFO::Creating boxplot for categorical data, Group vs GOLPDLCAT.PWY..superpathway.of.glycerol.degradation.to.1.3.propanediol## 2021-07-28 09:35:38 INFO::Creating boxplot for categorical data, Group vs PWY.6270..isoprene.biosynthesis.I## 2021-07-28 09:35:38 INFO::Creating boxplot for categorical data, Group vs PWY.5104..L.isoleucine.biosynthesis.IV## 2021-07-28 09:35:38 INFO::Creating boxplot for categorical data, Group vs PWY.7279..aerobic.respiration.II..cytochrome.c...yeast.## 2021-07-28 09:35:38 INFO::Creating boxplot for categorical data, Group vs PWY.6803..phosphatidylcholine.acyl.editing## 2021-07-28 09:35:38 INFO::Creating boxplot for categorical data, Group vs PWY.7199..pyrimidine.deoxyribonucleosides.salvage## 2021-07-28 09:35:38 INFO::Creating boxplot for categorical data, Group vs PWY.4984..urea.cycle## 2021-07-28 09:35:39 INFO::Creating boxplot for categorical data, Group vs PWY.7013..L.1.2.propanediol.degradation## 2021-07-28 09:35:39 INFO::Creating boxplot for categorical data, Group vs METSYN.PWY..L.homoserine.and.L.methionine.biosynthesis## 2021-07-28 09:35:39 INFO::Creating boxplot for categorical data, Group vs ASPASN.PWY..superpathway.of.L.aspartate.and.L.asparagine.biosynthesis## 2021-07-28 09:35:39 INFO::Creating boxplot for categorical data, Group vs FASYN.INITIAL.PWY..superpathway.of.fatty.acid.biosynthesis.initiation..E..coli.## 2021-07-28 09:35:39 INFO::Creating boxplot for categorical data, Group vs LPSSYN.PWY..superpathway.of.lipopolysaccharide.biosynthesis## 2021-07-28 09:35:39 INFO::Creating boxplot for categorical data, Group vs PWY.7196..superpathway.of.pyrimidine.ribonucleosides.salvage## 2021-07-28 09:35:39 INFO::Creating boxplot for categorical data, Group vs PWY.4242..pantothenate.and.coenzyme.A.biosynthesis.III## 2021-07-28 09:35:39 INFO::Creating boxplot for categorical data, Group vs PWY.6588..pyruvate.fermentation.to.acetone## 2021-07-28 09:35:39 INFO::Creating boxplot for categorical data, Group vs COBALSYN.PWY..adenosylcobalamin.salvage.from.cobinamide.I## 2021-07-28 09:35:39 INFO::Creating boxplot for categorical data, Group vs PWY.4041...gamma..glutamyl.cycle## 2021-07-28 09:35:39 INFO::Creating boxplot for categorical data, Group vs PWY.5005..biotin.biosynthesis.II## 2021-07-28 09:35:40 INFO::Creating boxplot for categorical data, Group vs PWY.6507..4.deoxy.L.threo.hex.4.enopyranuronate.degradation## 2021-07-28 09:35:40 INFO::Creating boxplot for categorical data, Group vs PWY.7282..4.amino.2.methyl.5.phosphomethylpyrimidine.biosynthesis..yeast.## 2021-07-28 09:35:40 INFO::Creating boxplot for categorical data, Group vs GLCMANNANAUT.PWY..superpathway.of.N.acetylglucosamine..N.acetylmannosamine.and.N.acetylneuraminate.degradation## 2021-07-28 09:35:40 INFO::Creating boxplot for categorical data, Group vs UNINTEGRATED## 2021-07-28 09:35:40 INFO::Creating boxplot for categorical data, Group vs P161.PWY..acetylene.degradation## 2021-07-28 09:35:40 INFO::Creating boxplot for categorical data, Group vs PWY.5695..urate.biosynthesis.inosine.5..phosphate.degradation## 2021-07-28 09:35:40 INFO::Creating boxplot for categorical data, Group vs PWY.724..superpathway.of.L.lysine..L.threonine.and.L.methionine.biosynthesis.II## 2021-07-28 09:35:40 INFO::Creating boxplot for categorical data, Group vs ARO.PWY..chorismate.biosynthesis.I## 2021-07-28 09:35:40 INFO::Creating boxplot for categorical data, Group vs PWY.5347..superpathway.of.L.methionine.biosynthesis..transsulfuration.## 2021-07-28 09:35:41 INFO::Creating boxplot for categorical data, Group vs PWY.5897..superpathway.of.menaquinol.11.biosynthesis## 2021-07-28 09:35:41 INFO::Creating boxplot for categorical data, Group vs PWY.5898..superpathway.of.menaquinol.12.biosynthesis## 2021-07-28 09:35:41 INFO::Creating boxplot for categorical data, Group vs PWY.5899..superpathway.of.menaquinol.13.biosynthesis## 2021-07-28 09:35:41 INFO::Creating boxplot for categorical data, Group vs PWY0.1297..superpathway.of.purine.deoxyribonucleosides.degradation## 2021-07-28 09:35:41 INFO::Creating boxplot for categorical data, Group vs GLUCARDEG.PWY..D.glucarate.degradation.I## 2021-07-28 09:35:41 INFO::Creating boxplot for categorical data, Group vs PWY.6125..superpathway.of.guanosine.nucleotides.de.novo.biosynthesis.II## 2021-07-28 09:35:41 INFO::Creating boxplot for categorical data, Group vs PWY.7220..adenosine.deoxyribonucleotides.de.novo.biosynthesis.II## 2021-07-28 09:35:41 INFO::Creating boxplot for categorical data, Group vs PWY.7222..guanosine.deoxyribonucleotides.de.novo.biosynthesis.II## 2021-07-28 09:35:41 INFO::Creating boxplot for categorical data, Group vs PWY.7323..superpathway.of.GDP.mannose.derived.O.antigen.building.blocks.biosynthesis## 2021-07-28 09:35:41 INFO::Creating boxplot for categorical data, Group vs GLUCONEO.PWY..gluconeogenesis.I## 2021-07-28 09:35:42 INFO::Creating boxplot for categorical data, Group vs COMPLETE.ARO.PWY..superpathway.of.aromatic.amino.acid.biosynthesis## 2021-07-28 09:35:42 INFO::Creating boxplot for categorical data, Group vs PWY.5415..catechol.degradation.I..meta.cleavage.pathway.## 2021-07-28 09:35:42 INFO::Creating boxplot for categorical data, Group vs PWY.7197..pyrimidine.deoxyribonucleotide.phosphorylation## 2021-07-28 09:35:42 INFO::Creating boxplot for categorical data, Group vs PWY.5030..L.histidine.degradation.III## 2021-07-28 09:35:42 INFO::Creating boxplot for categorical data, Group vs PWY.7184..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.I## 2021-07-28 09:35:42 INFO::Creating boxplot for categorical data, Group vs PWY66.399..gluconeogenesis.III## 2021-07-28 09:35:42 INFO::Creating boxplot for categorical data, Group vs PWY.621..sucrose.degradation.III..sucrose.invertase.## 2021-07-28 09:35:42 INFO::Creating boxplot for categorical data, Group vs PWY.6317..galactose.degradation.I..Leloir.pathway.## 2021-07-28 09:35:42 INFO::Creating boxplot for categorical data, Group vs PWY.6936..seleno.amino.acid.biosynthesis## 2021-07-28 09:35:42 INFO::Creating boxplot for categorical data, Group vs COLANSYN.PWY..colanic.acid.building.blocks.biosynthesis## 2021-07-28 09:35:43 INFO::Creating boxplot for categorical data, Group vs PWY66.422..D.galactose.degradation.V..Leloir.pathway.## 2021-07-28 09:35:43 INFO::Creating boxplot for categorical data, Group vs PWY0.1061..superpathway.of.L.alanine.biosynthesis## 2021-07-28 09:35:43 INFO::Creating boxplot for categorical data, Group vs PWY.6895..superpathway.of.thiamin.diphosphate.biosynthesis.II## 2021-07-28 09:35:43 INFO::Creating boxplot for categorical data, Group vs FOLSYN.PWY..superpathway.of.tetrahydrofolate.biosynthesis.and.salvage## 2021-07-28 09:35:43 INFO::Creating boxplot for categorical data, Group vs PYRIDNUCSAL.PWY..NAD.salvage.pathway.I## 2021-07-28 09:35:43 INFO::Creating boxplot for categorical data, Group vs PANTO.PWY..phosphopantothenate.biosynthesis.I## 2021-07-28 09:35:43 INFO::Creating boxplot for categorical data, Group vs FUCCAT.PWY..fucose.degradation## 2021-07-28 09:35:43 INFO::Creating boxplot for categorical data, Group vs PWY.6595..superpathway.of.guanosine.nucleotides.degradation..plants.## 2021-07-28 09:35:45 INFO::Plotting data for metadata number 2, Gender
## 2021-07-28 09:35:45 INFO::Creating boxplot for categorical data, Gender vs PWY0.1297..superpathway.of.purine.deoxyribonucleosides.degradation## 2021-07-28 09:35:45 INFO::Creating boxplot for categorical data, Gender vs PWY.7013..L.1.2.propanediol.degradation## 2021-07-28 09:35:45 INFO::Creating boxplot for categorical data, Gender vs NAD.BIOSYNTHESIS.II..NAD.salvage.pathway.II## 2021-07-28 09:35:45 INFO::Creating boxplot for categorical data, Gender vs PWY.5723..Rubisco.shunt## 2021-07-28 09:35:45 INFO::Creating boxplot for categorical data, Gender vs PPGPPMET.PWY..ppGpp.biosynthesis## 2021-07-28 09:35:45 INFO::Creating boxplot for categorical data, Gender vs PWY.6803..phosphatidylcholine.acyl.editing## 2021-07-28 09:35:45 INFO::Creating boxplot for categorical data, Gender vs PWY.5083..NAD.NADH.phosphorylation.and.dephosphorylation## 2021-07-28 09:35:45 INFO::Creating boxplot for categorical data, Gender vs P122.PWY..heterolactic.fermentation## 2021-07-28 09:35:45 INFO::Creating boxplot for categorical data, Gender vs PWY.5173..superpathway.of.acetyl.CoA.biosynthesis## 2021-07-28 09:35:46 INFO::Creating boxplot for categorical data, Gender vs PENTOSE.P.PWY..pentose.phosphate.pathway## 2021-07-28 09:35:46 INFO::Creating boxplot for categorical data, Gender vs PWY.6901..superpathway.of.glucose.and.xylose.degradation## 2021-07-28 09:35:46 INFO::Creating boxplot for categorical data, Gender vs PWY.5855..ubiquinol.7.biosynthesis..prokaryotic.## 2021-07-28 09:35:46 INFO::Creating boxplot for categorical data, Gender vs PWY.5856..ubiquinol.9.biosynthesis..prokaryotic.## 2021-07-28 09:35:46 INFO::Creating boxplot for categorical data, Gender vs PWY.5857..ubiquinol.10.biosynthesis..prokaryotic.## 2021-07-28 09:35:46 INFO::Creating boxplot for categorical data, Gender vs PWY.6708..ubiquinol.8.biosynthesis..prokaryotic.## 2021-07-28 09:35:46 INFO::Creating boxplot for categorical data, Gender vs GALACTARDEG.PWY..D.galactarate.degradation.I## 2021-07-28 09:35:46 INFO::Creating boxplot for categorical data, Gender vs GLUCARGALACTSUPER.PWY..superpathway.of.D.glucarate.and.D.galactarate.degradation## 2021-07-28 09:35:46 INFO::Creating boxplot for categorical data, Gender vs P4.PWY..superpathway.of.L.lysine..L.threonine.and.L.methionine.biosynthesis.I## 2021-07-28 09:35:46 INFO::Creating boxplot for categorical data, Gender vs HEXITOLDEGSUPER.PWY..superpathway.of.hexitol.degradation..bacteria.## 2021-07-28 09:35:46 INFO::Creating boxplot for categorical data, Gender vs PWY.4041...gamma..glutamyl.cycle## 2021-07-28 09:35:47 INFO::Creating boxplot for categorical data, Gender vs SO4ASSIM.PWY..sulfate.reduction.I..assimilatory.## 2021-07-28 09:35:47 INFO::Creating boxplot for categorical data, Gender vs FERMENTATION.PWY..mixed.acid.fermentation## 2021-07-28 09:35:47 INFO::Creating boxplot for categorical data, Gender vs PWY.5675..nitrate.reduction.V..assimilatory.## 2021-07-28 09:35:47 INFO::Creating boxplot for categorical data, Gender vs SULFATE.CYS.PWY..superpathway.of.sulfate.assimilation.and.cysteine.biosynthesis## 2021-07-28 09:35:47 INFO::Creating boxplot for categorical data, Gender vs P461.PWY..hexitol.fermentation.to.lactate..formate..ethanol.and.acetate## 2021-07-28 09:35:47 INFO::Creating boxplot for categorical data, Gender vs GLYCOLYSIS.E.D..superpathway.of.glycolysis.and.Entner.Doudoroff## 2021-07-28 09:35:47 INFO::Creating boxplot for categorical data, Gender vs PWY.7388..octanoyl..acyl.carrier.protein..biosynthesis..mitochondria..yeast.## 2021-07-28 09:35:47 INFO::Creating boxplot for categorical data, Gender vs DAPLYSINESYN.PWY..L.lysine.biosynthesis.I## 2021-07-28 09:35:47 INFO::Creating boxplot for categorical data, Gender vs P161.PWY..acetylene.degradation## 2021-07-28 09:35:47 INFO::Creating boxplot for categorical data, Gender vs PWY0.781..aspartate.superpathway## 2021-07-28 09:35:47 INFO::Creating boxplot for categorical data, Gender vs PWY0.1061..superpathway.of.L.alanine.biosynthesis## 2021-07-28 09:35:48 INFO::Creating boxplot for categorical data, Gender vs PWY.7204..pyridoxal.5..phosphate.salvage.II..plants.## 2021-07-28 09:35:48 INFO::Creating boxplot for categorical data, Gender vs GLUCARDEG.PWY..D.glucarate.degradation.I## 2021-07-28 09:35:48 INFO::Creating boxplot for categorical data, Gender vs HOMOSER.METSYN.PWY..L.methionine.biosynthesis.I## 2021-07-28 09:35:48 INFO::Creating boxplot for categorical data, Gender vs FASYN.INITIAL.PWY..superpathway.of.fatty.acid.biosynthesis.initiation..E..coli.## 2021-07-28 09:35:48 INFO::Creating boxplot for categorical data, Gender vs PWY.7664..oleate.biosynthesis.IV..anaerobic.## 2021-07-28 09:35:48 INFO::Creating boxplot for categorical data, Gender vs PWY.6282..palmitoleate.biosynthesis.I..from..5Z..dodec.5.enoate.## 2021-07-28 09:35:48 INFO::Creating boxplot for categorical data, Gender vs GLUCONEO.PWY..gluconeogenesis.I## 2021-07-28 09:35:48 INFO::Creating boxplot for categorical data, Gender vs PWY0.1241..ADP.L.glycero..beta..D.manno.heptose.biosynthesis## 2021-07-28 09:35:48 INFO::Creating boxplot for categorical data, Gender vs HEME.BIOSYNTHESIS.II..heme.biosynthesis.I..aerobic.## 2021-07-28 09:35:48 INFO::Creating boxplot for categorical data, Gender vs PWY0.1296..purine.ribonucleosides.degradation## 2021-07-28 09:35:49 INFO::Creating boxplot for categorical data, Gender vs ANAEROFRUCAT.PWY..homolactic.fermentation## 2021-07-28 09:35:49 INFO::Creating boxplot for categorical data, Gender vs MET.SAM.PWY..superpathway.of.S.adenosyl.L.methionine.biosynthesis## 2021-07-28 09:35:49 INFO::Creating boxplot for categorical data, Gender vs METSYN.PWY..L.homoserine.and.L.methionine.biosynthesis## 2021-07-28 09:35:49 INFO::Creating boxplot for categorical data, Gender vs NAGLIPASYN.PWY..lipid.IVA.biosynthesis## 2021-07-28 09:35:49 INFO::Creating boxplot for categorical data, Gender vs PWY.5347..superpathway.of.L.methionine.biosynthesis..transsulfuration.## 2021-07-28 09:35:49 INFO::Creating boxplot for categorical data, Gender vs PWY.6305..putrescine.biosynthesis.IV## 2021-07-28 09:35:49 INFO::Creating boxplot for categorical data, Gender vs P441.PWY..superpathway.of.N.acetylneuraminate.degradation## 2021-07-28 09:35:49 INFO::Creating boxplot for categorical data, Gender vs PWY.1269..CMP.3.deoxy.D.manno.octulosonate.biosynthesis.I## 2021-07-28 09:35:49 INFO::Creating boxplot for categorical data, Gender vs GOLPDLCAT.PWY..superpathway.of.glycerol.degradation.to.1.3.propanediol## 2021-07-28 09:35:49 INFO::Creating boxplot for categorical data, Gender vs PWY.6507..4.deoxy.L.threo.hex.4.enopyranuronate.degradation## 2021-07-28 09:35:50 INFO::Creating boxplot for categorical data, Gender vs PROTOCATECHUATE.ORTHO.CLEAVAGE.PWY..protocatechuate.degradation.II..ortho.cleavage.pathway.## 2021-07-28 09:35:50 INFO::Creating boxplot for categorical data, Gender vs PWY.7219..adenosine.ribonucleotides.de.novo.biosynthesis## 2021-07-28 09:35:50 INFO::Creating boxplot for categorical data, Gender vs PWY0.862...5Z..dodec.5.enoate.biosynthesis## 2021-07-28 09:35:50 INFO::Creating boxplot for categorical data, Gender vs PWY.5989..stearate.biosynthesis.II..bacteria.and.plants.## 2021-07-28 09:35:50 INFO::Creating boxplot for categorical data, Gender vs FASYN.ELONG.PWY..fatty.acid.elongation....saturated## 2021-07-28 09:35:50 INFO::Creating boxplot for categorical data, Gender vs PWY0.845..superpathway.of.pyridoxal.5..phosphate.biosynthesis.and.salvage## 2021-07-28 09:35:50 INFO::Creating boxplot for categorical data, Gender vs CALVIN.PWY..Calvin.Benson.Bassham.cycle## 2021-07-28 09:35:50 INFO::Creating boxplot for categorical data, Gender vs ANAGLYCOLYSIS.PWY..glycolysis.III..from.glucose.## 2021-07-28 09:35:50 INFO::Creating boxplot for categorical data, Gender vs GLUTORN.PWY..L.ornithine.biosynthesis## 2021-07-28 09:35:50 INFO::Creating boxplot for categorical data, Gender vs PHOSLIPSYN.PWY..superpathway.of.phospholipid.biosynthesis.I..bacteria.## 2021-07-28 09:35:50 INFO::Creating boxplot for categorical data, Gender vs PWY0.1586..peptidoglycan.maturation..meso.diaminopimelate.containing.## 2021-07-28 09:35:51 INFO::Creating boxplot for categorical data, Gender vs PWY.6121..5.aminoimidazole.ribonucleotide.biosynthesis.I## 2021-07-28 09:35:51 INFO::Creating boxplot for categorical data, Gender vs PWY.6122..5.aminoimidazole.ribonucleotide.biosynthesis.II## 2021-07-28 09:35:51 INFO::Creating boxplot for categorical data, Gender vs PWY.6277..superpathway.of.5.aminoimidazole.ribonucleotide.biosynthesis## 2021-07-28 09:35:51 INFO::Creating boxplot for categorical data, Gender vs TCA..TCA.cycle.I..prokaryotic.## 2021-07-28 09:35:51 INFO::Creating boxplot for categorical data, Gender vs GLYCOLYSIS..glycolysis.I..from.glucose.6.phosphate.## 2021-07-28 09:35:51 INFO::Creating boxplot for categorical data, Gender vs P125.PWY..superpathway.of..R.R..butanediol.biosynthesis## 2021-07-28 09:35:51 INFO::Creating boxplot for categorical data, Gender vs PWY.6895..superpathway.of.thiamin.diphosphate.biosynthesis.II## 2021-07-28 09:35:51 INFO::Creating boxplot for categorical data, Gender vs PWY.5484..glycolysis.II..from.fructose.6.phosphate.## 2021-07-28 09:35:51 INFO::Creating boxplot for categorical data, Gender vs SER.GLYSYN.PWY..superpathway.of.L.serine.and.glycine.biosynthesis.I## 2021-07-28 09:35:51 INFO::Creating boxplot for categorical data, Gender vs PWY.7663..gondoate.biosynthesis..anaerobic.## 2021-07-28 09:35:52 INFO::Creating boxplot for categorical data, Gender vs GLYCOGENSYNTH.PWY..glycogen.biosynthesis.I..from.ADP.D.Glucose.## 2021-07-28 09:35:52 INFO::Creating boxplot for categorical data, Gender vs PWY.5840..superpathway.of.menaquinol.7.biosynthesis## 2021-07-28 09:35:52 INFO::Creating boxplot for categorical data, Gender vs THISYN.PWY..superpathway.of.thiamin.diphosphate.biosynthesis.I## 2021-07-28 09:35:52 INFO::Creating boxplot for categorical data, Gender vs TRNA.CHARGING.PWY..tRNA.charging## 2021-07-28 09:35:52 INFO::Creating boxplot for categorical data, Gender vs PWY.5022..4.aminobutanoate.degradation.V## 2021-07-28 09:35:52 INFO::Creating boxplot for categorical data, Gender vs PWY.6609..adenine.and.adenosine.salvage.III## 2021-07-28 09:35:52 INFO::Creating boxplot for categorical data, Gender vs PWY.5695..urate.biosynthesis.inosine.5..phosphate.degradation## 2021-07-28 09:35:52 INFO::Creating boxplot for categorical data, Gender vs UBISYN.PWY..superpathway.of.ubiquinol.8.biosynthesis..prokaryotic.## 2021-07-28 09:35:52 INFO::Creating boxplot for categorical data, Gender vs PWY.1861..formaldehyde.assimilation.II..RuMP.Cycle.## 2021-07-28 09:35:52 INFO::Creating boxplot for categorical data, Gender vs GLYOXYLATE.BYPASS..glyoxylate.cycle## 2021-07-28 09:35:53 INFO::Creating boxplot for categorical data, Gender vs HISDEG.PWY..L.histidine.degradation.I## 2021-07-28 09:35:53 INFO::Creating boxplot for categorical data, Gender vs PWY.5154..L.arginine.biosynthesis.III..via.N.acetyl.L.citrulline.## 2021-07-28 09:35:53 INFO::Creating boxplot for categorical data, Gender vs NONOXIPENT.PWY..pentose.phosphate.pathway..non.oxidative.branch.## 2021-07-28 09:35:53 INFO::Creating boxplot for categorical data, Gender vs PWY.6891..thiazole.biosynthesis.II..Bacillus.## 2021-07-28 09:35:53 INFO::Creating boxplot for categorical data, Gender vs PWY0.1261..anhydromuropeptides.recycling## 2021-07-28 09:35:53 INFO::Creating boxplot for categorical data, Gender vs P108.PWY..pyruvate.fermentation.to.propanoate.I## 2021-07-28 09:35:53 INFO::Creating boxplot for categorical data, Gender vs PWY.7282..4.amino.2.methyl.5.phosphomethylpyrimidine.biosynthesis..yeast.## 2021-07-28 09:35:53 INFO::Creating boxplot for categorical data, Gender vs PWY.5913..TCA.cycle.VI..obligate.autotrophs.## 2021-07-28 09:35:53 INFO::Creating boxplot for categorical data, Gender vs GLYCOLYSIS.TCA.GLYOX.BYPASS..superpathway.of.glycolysis..pyruvate.dehydrogenase..TCA..and.glyoxylate.bypass## 2021-07-28 09:35:53 INFO::Creating boxplot for categorical data, Gender vs PWY.7221..guanosine.ribonucleotides.de.novo.biosynthesis## 2021-07-28 09:35:54 INFO::Creating boxplot for categorical data, Gender vs TCA.GLYOX.BYPASS..superpathway.of.glyoxylate.bypass.and.TCA## 2021-07-28 09:35:54 INFO::Creating boxplot for categorical data, Gender vs PYRIDOXSYN.PWY..pyridoxal.5..phosphate.biosynthesis.I## 2021-07-28 09:35:54 INFO::Creating boxplot for categorical data, Gender vs PWY.7392..taxadiene.biosynthesis..engineered.## 2021-07-28 09:35:54 INFO::Creating boxplot for categorical data, Gender vs PWY.6519..8.amino.7.oxononanoate.biosynthesis.I## 2021-07-28 09:35:54 INFO::Creating boxplot for categorical data, Gender vs PWY.6892..thiazole.biosynthesis.I..E..coli.## 2021-07-28 09:35:54 INFO::Creating boxplot for categorical data, Gender vs THISYNARA.PWY..superpathway.of.thiamin.diphosphate.biosynthesis.III..eukaryotes.## 2021-07-28 09:35:54 INFO::Creating boxplot for categorical data, Gender vs BIOTIN.BIOSYNTHESIS.PWY..biotin.biosynthesis.I## 2021-07-28 09:35:54 INFO::Creating boxplot for categorical data, Gender vs PWY.5667..CDP.diacylglycerol.biosynthesis.I## 2021-07-28 09:35:54 INFO::Creating boxplot for categorical data, Gender vs PWY.5897..superpathway.of.menaquinol.11.biosynthesis## 2021-07-28 09:35:54 INFO::Creating boxplot for categorical data, Gender vs PWY.5898..superpathway.of.menaquinol.12.biosynthesis## 2021-07-28 09:35:55 INFO::Creating boxplot for categorical data, Gender vs PWY.5899..superpathway.of.menaquinol.13.biosynthesis## 2021-07-28 09:35:55 INFO::Creating boxplot for categorical data, Gender vs PWY.6386..UDP.N.acetylmuramoyl.pentapeptide.biosynthesis.II..lysine.containing.## 2021-07-28 09:35:55 INFO::Creating boxplot for categorical data, Gender vs FUCCAT.PWY..fucose.degradation## 2021-07-28 09:35:55 INFO::Creating boxplot for categorical data, Gender vs PWY.5747..2.methylcitrate.cycle.II## 2021-07-28 09:35:55 INFO::Creating boxplot for categorical data, Gender vs PWY.7446..sulfoglycolysis## 2021-07-28 09:35:55 INFO::Creating boxplot for categorical data, Gender vs PWY0.42..2.methylcitrate.cycle.I## 2021-07-28 09:35:55 INFO::Creating boxplot for categorical data, Gender vs PWY.5838..superpathway.of.menaquinol.8.biosynthesis.I## 2021-07-28 09:35:55 INFO::Creating boxplot for categorical data, Gender vs PWY.5861..superpathway.of.demethylmenaquinol.8.biosynthesis## 2021-07-28 09:35:55 INFO::Creating boxplot for categorical data, Gender vs PWY.5918..superpathay.of.heme.biosynthesis.from.glutamate## 2021-07-28 09:35:55 INFO::Creating boxplot for categorical data, Gender vs PWY0.1319..CDP.diacylglycerol.biosynthesis.II## 2021-07-28 09:35:56 INFO::Creating boxplot for categorical data, Gender vs PWY0.1415..superpathway.of.heme.biosynthesis.from.uroporphyrinogen.III## 2021-07-28 09:35:56 INFO::Creating boxplot for categorical data, Gender vs PWY.5791..1.4.dihydroxy.2.naphthoate.biosynthesis.II..plants.## 2021-07-28 09:35:56 INFO::Creating boxplot for categorical data, Gender vs PWY.5837..1.4.dihydroxy.2.naphthoate.biosynthesis.I## 2021-07-28 09:35:56 INFO::Creating boxplot for categorical data, Gender vs PWY.6936..seleno.amino.acid.biosynthesis## 2021-07-28 09:35:56 INFO::Creating boxplot for categorical data, Gender vs PWY.621..sucrose.degradation.III..sucrose.invertase.## 2021-07-28 09:35:56 INFO::Creating boxplot for categorical data, Gender vs PWY0.162..superpathway.of.pyrimidine.ribonucleotides.de.novo.biosynthesis## 2021-07-28 09:35:56 INFO::Creating boxplot for categorical data, Gender vs ARGSYN.PWY..L.arginine.biosynthesis.I..via.L.ornithine.## 2021-07-28 09:35:56 INFO::Creating boxplot for categorical data, Gender vs PWY0.1298..superpathway.of.pyrimidine.deoxyribonucleosides.degradation## 2021-07-28 09:35:56 INFO::Creating boxplot for categorical data, Gender vs PWY.2941..L.lysine.biosynthesis.II## 2021-07-28 09:35:56 INFO::Creating boxplot for categorical data, Gender vs PWY.5659..GDP.mannose.biosynthesis## 2021-07-28 09:35:57 INFO::Creating boxplot for categorical data, Gender vs PWY.6630..superpathway.of.L.tyrosine.biosynthesis## 2021-07-28 09:35:57 INFO::Creating boxplot for categorical data, Gender vs PWY.7237..myo...chiro..and.scillo.inositol.degradation