MaAsLin2 finds associations between microbiome meta-omics features and complex metadata in population-scale epidemiological studies. The software includes multiple analysis methods (including support for multiple covariates and repeated measures) filtering, normalization, and transform options to customize analysis for your specific study.
Arguments
- data
a CollectionWithMetadata
- verbose
boolean indicating if timed logging is desired
- ...
additional arguments to pass to Maaslin2::Maaslin2
Details
The MicrobiomeDB wrapper for Maaslin2 will ignore samples where the fixed_effects variable
has a value of NA or the empty string ("").
Examples
maaslinOutput <- MicrobiomeDB::Maaslin2(
data = getCollection(
microbiomeData::DiabImmune,
'16S (V4) Genus (Relative taxonomic abundance analysis)'),
output = tempfile("maaslin"),
#min_prevalence = 0,
fixed_effects = 'delivery_mode',
analysis_method = "LM", # default LM
normalization = "TSS", # default TSS
transform = "LOG", # default LOG
plot_heatmap = FALSE,
plot_scatter = FALSE)
#> [1] "Creating output folder"
#> [1] "Creating output feature tables folder"
#> [1] "Creating output fits folder"
#> 2024-06-26 14:27:29.682172 INFO::Writing function arguments to log file
#> 2024-06-26 14:27:29.696927 INFO::Verifying options selected are valid
#> 2024-06-26 14:27:29.724798 INFO::Determining format of input files
#> 2024-06-26 14:27:29.726582 INFO::Input format is data samples as rows and metadata samples as rows
#> 2024-06-26 14:27:29.741943 INFO::Formula for fixed effects: expr ~ delivery_mode
#> 2024-06-26 14:27:29.742946 INFO::Filter data based on min abundance and min prevalence
#> 2024-06-26 14:27:29.743443 INFO::Total samples in data: 3184
#> 2024-06-26 14:27:29.743913 INFO::Min samples required with min abundance for a feature not to be filtered: 318.400000
#> 2024-06-26 14:27:29.774512 INFO::Total filtered features: 564
#> 2024-06-26 14:27:29.77556 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Achromobacter, Acidaminococcus, Acidibacter, Acidiphilium, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alcaligenes, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asaia, Asinibacterium, Asteroleplasma, Asticcacaulis, Aureimonas, Azospira, Bacillus, Bacteriovorax, Bdellovibrio, Belnapia, Bergeyella, Blastomonas, Bordetella, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Buttiauxella, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Caloribacterium, Candidatus.Arthromitus, Candidatus.Metachlamydia, Candidatus.Obscuribacter, Candidatus.Phytoplasma, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.15, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Corynebacterium, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Dechloromonas, Defluviicoccus, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desemzia, Desulfovibrio, Devosia, Diaphorobacter, Dickeya, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Edaphobaculum, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Erysipelotrichaceae.UCG.006, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Facklamia, Faecalicoccus, Faecalitalea, Falsochrobactrum, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavihumibacter, Flavobacterium, Floricoccus, Fluviicola, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Garciella, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gordonibacter, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Hymenobacter, Iamia, Ignavigranum, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Jeotgalicoccus, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnobacterium, Lachnospiraceae.AC2044.group, Lachnospiraceae.FE2018.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnospiraceae.XPB1014.group, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Mailhella, Marinilactibacillus, Marmoricola, Martelella, Marvinbryantia, Massilia, Megamonas, Merdibacter, Mesorhizobium, Methanobrevibacter, Methylibium, Methylobacillus, Methylobacterium.Methylorubrum, Methylorosula, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Muribaculum, Murimonas, Mycobacterium, Mycoplasma, Myxococcus, NK4A214.group, Nakamurella, Nannocystis, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neorhizobium, Neoscardovia, Nesterenkonia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, P3OB.42, Paenibacillus, Paeniclostridium, Paenisporosarcina, Paludicola, Papillibacter, Paraclostridium, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phascolarctobacterium, Phaseolibacter, Phocea, Phoenicibacter, Phyllobacterium, Piscinibacter, Planifilum, Plesiomonas, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Propionimicrobium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudocitrobacter, Pseudoflavonifractor, Pseudoglutamicibacter, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingoaurantiacus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinatimonas, Succiniclasticum, Succinivibrio, Sulfurospirillum, Synergistes, TM7x, Tannerella, Tatumella, Tepidimonas, Tepidiphilus, Tetragenococcus, Thermus, Timonella, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Vulcaniibacterium, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.67.14, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Acidaminococcaceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Armatimonadales, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Caulobacteraceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis..EUPATH_0009256_Bacteria_Actinobacteriota_Coriobacteriia_Coriobacteriales_Coriobacteriales_Incertae_Sedis_., unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Diplorickettsiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Fimbriimonadaceae, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Flavobacteriales, unclassified.Fusobacteriaceae, unclassified.Gaiellales, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.JI49D030, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.Lineage.IV, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Microbacteriaceae, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.NS9.marine.group, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Propionibacteriaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Alphaproteobacteria_Rhizobiales_Rhizobiales_Incertae_Sedis_., unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rickettsiales, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Sphingomonadaceae, unclassified.Staphylococcaceae, unclassified.Streptococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Verrucomicrobiota, unclassified.Victivallaceae, unclassified.W5053, unclassified.WPS.2, unclassified.Weeksellaceae, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97
#> 2024-06-26 14:27:29.78355 INFO::Total filtered features with variance filtering: 0
#> 2024-06-26 14:27:29.78413 INFO::Filtered feature names from variance filtering:
#> 2024-06-26 14:27:29.784617 INFO::Running selected normalization method: TSS
#> 2024-06-26 14:27:29.846918 INFO::Applying z-score to standardize continuous metadata
#> 2024-06-26 14:27:29.855053 INFO::Running selected transform method: LOG
#> 2024-06-26 14:27:29.929403 INFO::Running selected analysis method: LM
#> 2024-06-26 14:27:29.935358 INFO::Fitting model to feature number 1, Actinomyces
#> 2024-06-26 14:27:30.68271 INFO::Fitting model to feature number 2, Agathobacter
#> 2024-06-26 14:27:30.688327 INFO::Fitting model to feature number 3, Akkermansia
#> 2024-06-26 14:27:30.693074 INFO::Fitting model to feature number 4, Alistipes
#> 2024-06-26 14:27:30.697743 INFO::Fitting model to feature number 5, Anaerostipes
#> 2024-06-26 14:27:30.702388 INFO::Fitting model to feature number 6, Atopobium
#> 2024-06-26 14:27:30.706916 INFO::Fitting model to feature number 7, Bacteroides
#> 2024-06-26 14:27:30.711432 INFO::Fitting model to feature number 8, Barnesiella
#> 2024-06-26 14:27:30.715945 INFO::Fitting model to feature number 9, Bifidobacterium
#> 2024-06-26 14:27:30.72057 INFO::Fitting model to feature number 10, Bilophila
#> 2024-06-26 14:27:30.725066 INFO::Fitting model to feature number 11, Blautia
#> 2024-06-26 14:27:30.729595 INFO::Fitting model to feature number 12, Butyricicoccus
#> 2024-06-26 14:27:30.734111 INFO::Fitting model to feature number 13, CAG.352
#> 2024-06-26 14:27:30.738599 INFO::Fitting model to feature number 14, Campylobacter
#> 2024-06-26 14:27:30.743064 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group
#> 2024-06-26 14:27:30.74753 INFO::Fitting model to feature number 16, Clostridioides
#> 2024-06-26 14:27:30.75198 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1
#> 2024-06-26 14:27:30.756477 INFO::Fitting model to feature number 18, Colidextribacter
#> 2024-06-26 14:27:30.760958 INFO::Fitting model to feature number 19, Collinsella
#> 2024-06-26 14:27:30.765425 INFO::Fitting model to feature number 20, Coprobacillus
#> 2024-06-26 14:27:30.769905 INFO::Fitting model to feature number 21, Coprococcus
#> 2024-06-26 14:27:30.774372 INFO::Fitting model to feature number 22, DTU089
#> 2024-06-26 14:27:30.778799 INFO::Fitting model to feature number 23, Dialister
#> 2024-06-26 14:27:30.783242 INFO::Fitting model to feature number 24, Dorea
#> 2024-06-26 14:27:30.787678 INFO::Fitting model to feature number 25, Eggerthella
#> 2024-06-26 14:27:30.792142 INFO::Fitting model to feature number 26, Eisenbergiella
#> 2024-06-26 14:27:30.796595 INFO::Fitting model to feature number 27, Enterococcus
#> 2024-06-26 14:27:30.801078 INFO::Fitting model to feature number 28, Erysipelatoclostridium
#> 2024-06-26 14:27:30.805504 INFO::Fitting model to feature number 29, Erysipelotrichaceae.UCG.003
#> 2024-06-26 14:27:30.809915 INFO::Fitting model to feature number 30, Escherichia.Shigella
#> 2024-06-26 14:27:30.814348 INFO::Fitting model to feature number 31, Faecalibacterium
#> 2024-06-26 14:27:30.818783 INFO::Fitting model to feature number 32, Family.XIII.AD3011.group
#> 2024-06-26 14:27:30.823269 INFO::Fitting model to feature number 33, Flavonifractor
#> 2024-06-26 14:27:30.827777 INFO::Fitting model to feature number 34, Fusicatenibacter
#> 2024-06-26 14:27:30.832203 INFO::Fitting model to feature number 35, Fusobacterium
#> 2024-06-26 14:27:30.836623 INFO::Fitting model to feature number 36, Gemella
#> 2024-06-26 14:27:30.841048 INFO::Fitting model to feature number 37, Granulicatella
#> 2024-06-26 14:27:30.845501 INFO::Fitting model to feature number 38, Haemophilus
#> 2024-06-26 14:27:30.849955 INFO::Fitting model to feature number 39, Holdemania
#> 2024-06-26 14:27:30.854382 INFO::Fitting model to feature number 40, Hungatella
#> 2024-06-26 14:27:30.858769 INFO::Fitting model to feature number 41, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis.
#> 2024-06-26 14:27:30.863179 INFO::Fitting model to feature number 42, Intestinibacter
#> 2024-06-26 14:27:30.867609 INFO::Fitting model to feature number 43, Intestinimonas
#> 2024-06-26 14:27:30.872024 INFO::Fitting model to feature number 44, Klebsiella
#> 2024-06-26 14:27:30.876467 INFO::Fitting model to feature number 45, Lachnoclostridium
#> 2024-06-26 14:27:30.880857 INFO::Fitting model to feature number 46, Lachnospira
#> 2024-06-26 14:27:30.886671 INFO::Fitting model to feature number 47, Lachnospiraceae.FCS020.group
#> 2024-06-26 14:27:30.892635 INFO::Fitting model to feature number 48, Lachnospiraceae.ND3007.group
#> 2024-06-26 14:27:30.898595 INFO::Fitting model to feature number 49, Lachnospiraceae.NK4A136.group
#> 2024-06-26 14:27:30.904554 INFO::Fitting model to feature number 50, Lachnospiraceae.UCG.001
#> 2024-06-26 14:27:30.910494 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.004
#> 2024-06-26 14:27:30.916446 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.009
#> 2024-06-26 14:27:30.922379 INFO::Fitting model to feature number 53, Lachnospiraceae.UCG.010
#> 2024-06-26 14:27:30.928372 INFO::Fitting model to feature number 54, Lactobacillus
#> 2024-06-26 14:27:30.93433 INFO::Fitting model to feature number 55, Lactococcus
#> 2024-06-26 14:27:30.940294 INFO::Fitting model to feature number 56, Mannheimia
#> 2024-06-26 14:27:30.946261 INFO::Fitting model to feature number 57, Megasphaera
#> 2024-06-26 14:27:30.952261 INFO::Fitting model to feature number 58, Monoglobus
#> 2024-06-26 14:27:30.958254 INFO::Fitting model to feature number 59, Neisseria
#> 2024-06-26 14:27:30.964304 INFO::Fitting model to feature number 60, Odoribacter
#> 2024-06-26 14:27:30.970278 INFO::Fitting model to feature number 61, Oscillibacter
#> 2024-06-26 14:27:30.97627 INFO::Fitting model to feature number 62, Oscillospira
#> 2024-06-26 14:27:30.982278 INFO::Fitting model to feature number 63, Parabacteroides
#> 2024-06-26 14:27:30.988256 INFO::Fitting model to feature number 64, Parasutterella
#> 2024-06-26 14:27:30.99433 INFO::Fitting model to feature number 65, Prevotella
#> 2024-06-26 14:27:31.00039 INFO::Fitting model to feature number 66, Pseudomonas
#> 2024-06-26 14:27:31.006396 INFO::Fitting model to feature number 67, Romboutsia
#> 2024-06-26 14:27:31.012378 INFO::Fitting model to feature number 68, Roseburia
#> 2024-06-26 14:27:31.018394 INFO::Fitting model to feature number 69, Rothia
#> 2024-06-26 14:27:31.024542 INFO::Fitting model to feature number 70, Ruminococcus
#> 2024-06-26 14:27:31.030638 INFO::Fitting model to feature number 71, Sellimonas
#> 2024-06-26 14:27:31.03677 INFO::Fitting model to feature number 72, Solobacterium
#> 2024-06-26 14:27:31.042808 INFO::Fitting model to feature number 73, Staphylococcus
#> 2024-06-26 14:27:31.04881 INFO::Fitting model to feature number 74, Streptococcus
#> 2024-06-26 14:27:31.055039 INFO::Fitting model to feature number 75, Subdoligranulum
#> 2024-06-26 14:27:31.061346 INFO::Fitting model to feature number 76, Sutterella
#> 2024-06-26 14:27:31.067462 INFO::Fitting model to feature number 77, Terrisporobacter
#> 2024-06-26 14:27:31.073571 INFO::Fitting model to feature number 78, Turicibacter
#> 2024-06-26 14:27:31.079634 INFO::Fitting model to feature number 79, Tuzzerella
#> 2024-06-26 14:27:31.085753 INFO::Fitting model to feature number 80, Tyzzerella
#> 2024-06-26 14:27:31.091835 INFO::Fitting model to feature number 81, UBA1819
#> 2024-06-26 14:27:31.097953 INFO::Fitting model to feature number 82, UCG.002
#> 2024-06-26 14:27:31.104068 INFO::Fitting model to feature number 83, UCG.003
#> 2024-06-26 14:27:31.110127 INFO::Fitting model to feature number 84, UCG.005
#> 2024-06-26 14:27:31.116212 INFO::Fitting model to feature number 85, Veillonella
#> 2024-06-26 14:27:31.12236 INFO::Fitting model to feature number 86, X.Clostridium..innocuum.group
#> 2024-06-26 14:27:31.128447 INFO::Fitting model to feature number 87, X.Eubacterium..eligens.group
#> 2024-06-26 14:27:31.142886 INFO::Fitting model to feature number 88, X.Eubacterium..fissicatena.group
#> 2024-06-26 14:27:31.14741 INFO::Fitting model to feature number 89, X.Eubacterium..hallii.group
#> 2024-06-26 14:27:31.151888 INFO::Fitting model to feature number 90, X.Eubacterium..siraeum.group
#> 2024-06-26 14:27:31.156343 INFO::Fitting model to feature number 91, X.Eubacterium..ventriosum.group
#> 2024-06-26 14:27:31.160805 INFO::Fitting model to feature number 92, X.Eubacterium..xylanophilum.group
#> 2024-06-26 14:27:31.165271 INFO::Fitting model to feature number 93, X.Ruminococcus..gauvreauii.group
#> 2024-06-26 14:27:31.169882 INFO::Fitting model to feature number 94, X.Ruminococcus..gnavus.group
#> 2024-06-26 14:27:31.174381 INFO::Fitting model to feature number 95, X.Ruminococcus..torques.group
#> 2024-06-26 14:27:31.178882 INFO::Fitting model to feature number 96, unclassified.Chloroplast
#> 2024-06-26 14:27:31.183355 INFO::Fitting model to feature number 97, unclassified.Clostridia.UCG.014
#> 2024-06-26 14:27:31.187812 INFO::Fitting model to feature number 98, unclassified.Clostridia
#> 2024-06-26 14:27:31.192285 INFO::Fitting model to feature number 99, unclassified.Clostridia.vadinBB60.group
#> 2024-06-26 14:27:31.196805 INFO::Fitting model to feature number 100, unclassified.Gastranaerophilales
#> 2024-06-26 14:27:31.201344 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae
#> 2024-06-26 14:27:31.205845 INFO::Fitting model to feature number 102, unclassified.Mitochondria
#> 2024-06-26 14:27:31.210337 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae
#> 2024-06-26 14:27:31.214799 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus
#> 2024-06-26 14:27:31.219235 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales
#> 2024-06-26 14:27:31.223686 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae
#> 2024-06-26 14:27:31.228182 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group
#> 2024-06-26 14:27:31.247113 INFO::Counting total values for each feature
#> 2024-06-26 14:27:31.252876 INFO::Writing filtered data to file /tmp/Rtmp1DvrdC/maaslin17d61689e91c/features/filtered_data.tsv
#> 2024-06-26 14:27:31.470656 INFO::Writing filtered, normalized data to file /tmp/Rtmp1DvrdC/maaslin17d61689e91c/features/filtered_data_norm.tsv
#> 2024-06-26 14:27:31.691205 INFO::Writing filtered, normalized, transformed data to file /tmp/Rtmp1DvrdC/maaslin17d61689e91c/features/filtered_data_norm_transformed.tsv
#> 2024-06-26 14:27:32.052359 INFO::Writing residuals to file /tmp/Rtmp1DvrdC/maaslin17d61689e91c/fits/residuals.rds
#> 2024-06-26 14:27:32.123329 INFO::Writing fitted values to file /tmp/Rtmp1DvrdC/maaslin17d61689e91c/fits/fitted.rds
#> 2024-06-26 14:27:32.147751 INFO::Writing all results to file (ordered by increasing q-values): /tmp/Rtmp1DvrdC/maaslin17d61689e91c/all_results.tsv
#> 2024-06-26 14:27:32.149597 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): /tmp/Rtmp1DvrdC/maaslin17d61689e91c/significant_results.tsv