diff --git a/articles/alphadiv.html b/articles/alphadiv.html index c2a1e63..f6cc175 100644 --- a/articles/alphadiv.html +++ b/articles/alphadiv.html @@ -166,11 +166,11 @@

Shannon Diversity Index## get an alpha diversity ComputeResult alphaDivOutput <- alphaDiv(genus, method = 'shannon') #> -#> 2024-05-29 19:15:40.027972 Received df table with 741 samples and 226 taxa. +#> 2024-05-29 19:45:03.766484 Received df table with 741 samples and 226 taxa. #> -#> 2024-05-29 19:15:40.065382 shannon alpha diversity computation complete. +#> 2024-05-29 19:45:03.789404 shannon alpha diversity computation complete. #> -#> 2024-05-29 19:15:40.080644 Alpha diversity computation completed with parameters method= shannon +#> 2024-05-29 19:45:03.804795 Alpha diversity computation completed with parameters method= shannon

Simpson Diversity Index @@ -184,11 +184,11 @@

Simpson Diversity Indexgenus <- getCollection(microbiomeData::HMP_MGX, 'Shotgun metagenomics Genus (Relative taxonomic abundance analysis)') alphaDivOutput <- alphaDiv(genus, method = 'simpson') #> -#> 2024-05-29 19:15:40.176462 Received df table with 741 samples and 226 taxa. +#> 2024-05-29 19:45:03.898376 Received df table with 741 samples and 226 taxa. #> -#> 2024-05-29 19:15:40.199764 simpson alpha diversity computation complete. +#> 2024-05-29 19:45:03.920918 simpson alpha diversity computation complete. #> -#> 2024-05-29 19:15:40.205054 Alpha diversity computation completed with parameters method= simpson

+#> 2024-05-29 19:45:03.926178 Alpha diversity computation completed with parameters method= simpson

Species Evenness @@ -202,11 +202,11 @@

Species Evennessgenus <- getCollection(microbiomeData::HMP_MGX, 'Shotgun metagenomics Genus (Relative taxonomic abundance analysis)') alphaDivOutput <- alphaDiv(genus, method = 'evenness') #> -#> 2024-05-29 19:15:40.29267 Received df table with 741 samples and 226 taxa. +#> 2024-05-29 19:45:04.01165 Received df table with 741 samples and 226 taxa. #> -#> 2024-05-29 19:15:40.322748 evenness alpha diversity computation complete. +#> 2024-05-29 19:45:04.041403 evenness alpha diversity computation complete. #> -#> 2024-05-29 19:15:40.325971 Alpha diversity computation completed with parameters method= evenness

+#> 2024-05-29 19:45:04.044687 Alpha diversity computation completed with parameters method= evenness
diff --git a/articles/alphadiv_files/figure-html/unnamed-chunk-5-1.png b/articles/alphadiv_files/figure-html/unnamed-chunk-5-1.png index b2aabc3..ac3885f 100644 Binary files a/articles/alphadiv_files/figure-html/unnamed-chunk-5-1.png and b/articles/alphadiv_files/figure-html/unnamed-chunk-5-1.png differ diff --git a/articles/betadiv.html b/articles/betadiv.html index a64fc78..fc96423 100644 --- a/articles/betadiv.html +++ b/articles/betadiv.html @@ -173,13 +173,13 @@

Bray-Curtis Dissimilarity## get a betaDiv ComputeResult betaDiv <- betaDiv(HMP_MGX_species, method = "bray") #> -#> 2024-05-29 19:15:53.987558 Received df table with 741 samples and 731 taxa. +#> 2024-05-29 19:45:17.810675 Received df table with 741 samples and 731 taxa. #> -#> 2024-05-29 19:15:54.330892 Computed dissimilarity matrix. +#> 2024-05-29 19:45:18.153009 Computed dissimilarity matrix. #> -#> 2024-05-29 19:15:55.300075 Finished ordination step. +#> 2024-05-29 19:45:19.095503 Finished ordination step. #> -#> 2024-05-29 19:15:55.333184 Beta diversity computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = bray , k = 2 , verbose = TRUE

+#> 2024-05-29 19:45:19.125308 Beta diversity computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = bray , k = 2 , verbose = TRUE

Jaccard Dissimilarity @@ -191,13 +191,13 @@

Jaccard DissimilarityHMP_MGX_species <- getCollection(microbiomeData::HMP_MGX, 'Shotgun metagenomics Species (Relative taxonomic abundance analysis)') betaDiv <- betaDiv(HMP_MGX_species, method = "jaccard") #> -#> 2024-05-29 19:15:55.486934 Received df table with 741 samples and 731 taxa. +#> 2024-05-29 19:45:19.278769 Received df table with 741 samples and 731 taxa. #> -#> 2024-05-29 19:15:55.807774 Computed dissimilarity matrix. +#> 2024-05-29 19:45:19.612632 Computed dissimilarity matrix. #> -#> 2024-05-29 19:15:55.995823 Finished ordination step. +#> 2024-05-29 19:45:19.792349 Finished ordination step. #> -#> 2024-05-29 19:15:56.006563 Beta diversity computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = jaccard , k = 2 , verbose = TRUE

+#> 2024-05-29 19:45:19.803358 Beta diversity computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = jaccard , k = 2 , verbose = TRUE

Jensen-Shannon Divergence (JSD) @@ -210,13 +210,13 @@

Jensen-Shannon Divergence (JSD)HMP_MGX_species <- getCollection(microbiomeData::HMP_MGX, 'Shotgun metagenomics Species (Relative taxonomic abundance analysis)') betaDiv <- betaDiv(HMP_MGX_species, method = "jsd") #> -#> 2024-05-29 19:15:56.150185 Received df table with 741 samples and 731 taxa. +#> 2024-05-29 19:45:19.94657 Received df table with 741 samples and 731 taxa. #> -#> 2024-05-29 19:16:03.228924 Computed dissimilarity matrix. +#> 2024-05-29 19:45:27.013699 Computed dissimilarity matrix. #> -#> 2024-05-29 19:16:03.432243 Finished ordination step. +#> 2024-05-29 19:45:27.202883 Finished ordination step. #> -#> 2024-05-29 19:16:03.438457 Beta diversity computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = jsd , k = 2 , verbose = TRUE

+#> 2024-05-29 19:45:27.209171 Beta diversity computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = jsd , k = 2 , verbose = TRUE

Principal Coordinate Analysis (PCoA): diff --git a/articles/betadiv_files/figure-html/unnamed-chunk-5-1.png b/articles/betadiv_files/figure-html/unnamed-chunk-5-1.png index 2c82cbe..8fccd4a 100644 Binary files a/articles/betadiv_files/figure-html/unnamed-chunk-5-1.png and b/articles/betadiv_files/figure-html/unnamed-chunk-5-1.png differ diff --git a/articles/correlation.html b/articles/correlation.html index a88485d..e199903 100644 --- a/articles/correlation.html +++ b/articles/correlation.html @@ -231,17 +231,17 @@

Spearman Correlation## it is simply exemplary. Always look at your data! species_vs_metadata <- correlation(HMP_V3V5_species, method = 'spearman') #> -#> 2024-05-29 19:16:20.559966 Removed 1 records with no data. +#> 2024-05-29 19:45:44.436455 Removed 1 records with no data. #> -#> 2024-05-29 19:16:20.596572 Removed 1 records with no data. +#> 2024-05-29 19:45:44.47219 Removed 1 records with no data. #> -#> 2024-05-29 19:16:20.633135 Removed 1 records with no data. +#> 2024-05-29 19:45:44.508659 Removed 1 records with no data. #> -#> 2024-05-29 19:16:23.026126 Completed correlation with method=spearman. Formatting results. +#> 2024-05-29 19:45:46.901617 Completed correlation with method=spearman. Formatting results. #> -#> 2024-05-29 19:16:23.02706 Received df table with 5461 samples and 137 features with values. +#> 2024-05-29 19:45:46.902671 Received df table with 5461 samples and 137 features with values. #> -#> 2024-05-29 19:16:23.031335 Correlation computation completed with parameters recordIdColumn= 16S_rRNA_(V3-V5)_assay_Id , method = spearman

+#> 2024-05-29 19:45:46.907404 Correlation computation completed with parameters recordIdColumn= 16S_rRNA_(V3-V5)_assay_Id , method = spearman

Pearson Correlation @@ -258,21 +258,21 @@

Pearson Correlation## it is simply exemplary. Always look at your data! pathway_vs_species <- correlation(HMP_MGX_species, HMP_MGX_pathways, method = 'pearson') #> -#> 2024-05-29 19:16:23.549514 Removed 7 records with no data. +#> 2024-05-29 19:45:47.423034 Removed 7 records with no data. #> -#> 2024-05-29 19:16:23.578317 Removed 7 records with no data. +#> 2024-05-29 19:45:47.452204 Removed 7 records with no data. #> -#> 2024-05-29 19:16:23.702107 Removed 7 records with no data. +#> 2024-05-29 19:45:47.57837 Removed 7 records with no data. #> -#> 2024-05-29 19:16:23.716146 Received first df table with 734 samples and 325 features with values. +#> 2024-05-29 19:45:47.589441 Received first df table with 734 samples and 325 features with values. #> -#> 2024-05-29 19:16:23.716566 Received second df table with 741 samples and 371 features with values. +#> 2024-05-29 19:45:47.589732 Received second df table with 741 samples and 371 features with values. #> -#> 2024-05-29 19:16:23.716918 Found 734 samples in common between data1 and data2. Only these samples will be used. +#> 2024-05-29 19:45:47.589983 Found 734 samples in common between data1 and data2. Only these samples will be used. #> -#> 2024-05-29 19:16:24.140233 Completed correlation with method=pearson. Formatting results. +#> 2024-05-29 19:45:48.007937 Completed correlation with method=pearson. Formatting results. #> -#> 2024-05-29 19:16:24.145993 Correlation computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = pearson

+#> 2024-05-29 19:45:48.013822 Correlation computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = pearson
diff --git a/articles/ranked-abundance.html b/articles/ranked-abundance.html index 1e4b43d..e43a311 100644 --- a/articles/ranked-abundance.html +++ b/articles/ranked-abundance.html @@ -181,38 +181,38 @@

How to Find Ranked Relative Abun ## top 10 taxa by max relative abundance across all samples rankedAbund <- rankedAbundance(HMP_MGX_species, method = "max", cutoff = 10) #> -#> 2024-05-29 19:16:38.60142 Received df table with 741 samples and 731 taxa. +#> 2024-05-29 19:46:02.30343 Received df table with 741 samples and 731 taxa. #> -#> 2024-05-29 19:16:38.634538 Finished ranking taxa +#> 2024-05-29 19:46:02.336498 Finished ranking taxa #> -#> 2024-05-29 19:16:38.654815 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = max , cutoff = 10 , naToZero = TRUE , verbose = TRUE

+#> 2024-05-29 19:46:02.357058 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = max , cutoff = 10 , naToZero = TRUE , verbose = TRUE 
 ## top 8 taxa by median relative abundance across all samples
 rankedAbund <- rankedAbundance(HMP_MGX_species, method = "median", cutoff = 8)
 #> 
-#> 2024-05-29 19:16:39.400432 Received df table with 741 samples and 731 taxa.
+#> 2024-05-29 19:46:03.121664 Received df table with 741 samples and 731 taxa.
 #> 
-#> 2024-05-29 19:16:39.422565 Finished ranking taxa
+#> 2024-05-29 19:46:03.144673 Finished ranking taxa
 #> 
-#> 2024-05-29 19:16:39.431385 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = median , cutoff = 8 , naToZero =  TRUE , verbose = TRUE
+#> 2024-05-29 19:46:03.153606 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = median , cutoff = 8 , naToZero = TRUE , verbose = TRUE 
 ## top 20 taxa by third quartile relative abundance across all samples
 rankedAbund <- rankedAbundance(HMP_MGX_species, method = "q3", cutoff = 20)
 #> 
-#> 2024-05-29 19:16:39.460068 Received df table with 741 samples and 731 taxa.
+#> 2024-05-29 19:46:03.182232 Received df table with 741 samples and 731 taxa.
 #> 
-#> 2024-05-29 19:16:39.569929 Finished ranking taxa
+#> 2024-05-29 19:46:03.300048 Finished ranking taxa
 #> 
-#> 2024-05-29 19:16:39.576298 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = q3 , cutoff = 20 , naToZero =  TRUE , verbose = TRUE
+#> 2024-05-29 19:46:03.306281 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = q3 , cutoff = 20 , naToZero = TRUE , verbose = TRUE 
 ## top 10 taxa by greatest variance in relative abundance across all samples
 rankedAbund <- rankedAbundance(HMP_MGX_species, method = "variance", cutoff = 10)
 #> 
-#> 2024-05-29 19:16:39.594134 Received df table with 741 samples and 731 taxa.
+#> 2024-05-29 19:46:03.324066 Received df table with 741 samples and 731 taxa.
 #> 
-#> 2024-05-29 19:16:39.626253 Finished ranking taxa
+#> 2024-05-29 19:46:03.361709 Finished ranking taxa
 #> 
-#> 2024-05-29 19:16:39.631461 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = variance , cutoff = 10 , naToZero =  TRUE , verbose = TRUE
+#> 2024-05-29 19:46:03.367187 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = variance , cutoff = 10 , naToZero = TRUE , verbose = TRUE

Visualizing Ranked Relative Abundances diff --git a/articles/ranked-abundance_files/figure-html/unnamed-chunk-3-1.png b/articles/ranked-abundance_files/figure-html/unnamed-chunk-3-1.png index bac9dce..ceb9d85 100644 Binary files a/articles/ranked-abundance_files/figure-html/unnamed-chunk-3-1.png and b/articles/ranked-abundance_files/figure-html/unnamed-chunk-3-1.png differ diff --git a/articles/self-correlation.html b/articles/self-correlation.html index c2da7ec..5eddabf 100644 --- a/articles/self-correlation.html +++ b/articles/self-correlation.html @@ -200,18 +200,18 @@

How are Correlations Calculated?## these methods can be used with other data types as well farmm_metabolomics <- getCollection(microbiomeData::FARMM, "Metabolomics Mass spectrometry assay") #> -#> 2024-05-29 19:16:52.768823 Integer values detected. Converting collection to AbsoluteAbundanceData

+#> 2024-05-29 19:46:16.587501 Integer values detected. Converting collection to AbsoluteAbundanceData 
 
 ## get a self correlation ComputeResult
 ## methods spearman and pearson are options here as well, for data known to not be compositional
 selfCorrelation_metabolomics <- selfCorrelation(farmm_metabolomics, method='spearman')
 #> 
-#> 2024-05-29 19:16:54.821399 Completed correlation with method=spearman. Formatting results.
+#> 2024-05-29 19:46:18.657134 Completed correlation with method=spearman. Formatting results.
 #> 
-#> 2024-05-29 19:16:54.943483 Received df table with 150 samples and 479 features with abundances.
+#> 2024-05-29 19:46:18.784305 Received df table with 150 samples and 479 features with abundances.
 #> 
-#> 2024-05-29 19:16:54.947876 Correlation computation completed with parameters recordIdColumn= Mass_spectrometry_assay_Id , method =  spearman
+#> 2024-05-29 19:46:18.788878 Correlation computation completed with parameters recordIdColumn= Mass_spectrometry_assay_Id , method = spearman

Interpreting Results diff --git a/index.html b/index.html index ed5d12e..735261b 100644 --- a/index.html +++ b/index.html @@ -72,7 +72,7 @@

MicrobiomeDB

-

An R package containing all of the data from MicrobiomeDB.org, and tools for analyzing and visualizing the same.

+

A suite of R packages containing all of the data from MicrobiomeDB.org, and tools for analyzing and visualizing the same.

Installation

diff --git a/pkgdown.yml b/pkgdown.yml index 1432ff6..f948545 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -7,7 +7,7 @@ articles: correlation: correlation.html ranked-abundance: ranked-abundance.html self-correlation: self-correlation.html -last_built: 2024-05-29T18:54Z +last_built: 2024-05-29T19:24Z urls: reference: https://microbiomedb.github.io/MicrobiomeDB/reference article: https://microbiomedb.github.io/MicrobiomeDB/articles diff --git a/reference/Maaslin2.html b/reference/Maaslin2.html index 838c0cb..94dcf18 100644 --- a/reference/Maaslin2.html +++ b/reference/Maaslin2.html @@ -113,137 +113,137 @@

Examples#> [1] "Creating output folder" #> [1] "Creating output feature tables folder" #> [1] "Creating output fits folder" -#> 2024-05-29 18:54:57.562905 INFO::Writing function arguments to log file -#> 2024-05-29 18:54:57.578155 INFO::Verifying options selected are valid -#> 2024-05-29 18:54:57.607544 INFO::Determining format of input files -#> 2024-05-29 18:54:57.609495 INFO::Input format is data samples as rows and metadata samples as rows -#> 2024-05-29 18:54:57.625292 INFO::Formula for fixed effects: expr ~ delivery_mode -#> 2024-05-29 18:54:57.626482 INFO::Filter data based on min abundance and min prevalence -#> 2024-05-29 18:54:57.626988 INFO::Total samples in data: 3184 -#> 2024-05-29 18:54:57.627444 INFO::Min samples required with min abundance for a feature not to be filtered: 318.400000 -#> 2024-05-29 18:54:57.659748 INFO::Total filtered features: 564 -#> 2024-05-29 18:54:57.660913 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 -#> 2024-05-29 18:54:57.66912 INFO::Total filtered features with variance filtering: 0 -#> 2024-05-29 18:54:57.669881 INFO::Filtered feature names from variance filtering: -#> 2024-05-29 18:54:57.670354 INFO::Running selected normalization method: TSS -#> 2024-05-29 18:54:57.732666 INFO::Applying z-score to standardize continuous metadata -#> 2024-05-29 18:54:57.740981 INFO::Running selected transform method: LOG -#> 2024-05-29 18:54:57.815492 INFO::Running selected analysis method: LM -#> 2024-05-29 18:54:57.821778 INFO::Fitting model to feature number 1, Actinomyces -#> 2024-05-29 18:54:57.853598 INFO::Fitting model to feature number 2, Agathobacter -#> 2024-05-29 18:54:57.858835 INFO::Fitting model to feature number 3, Akkermansia -#> 2024-05-29 18:54:57.863948 INFO::Fitting model to feature number 4, Alistipes -#> 2024-05-29 18:54:57.869185 INFO::Fitting model to feature number 5, Anaerostipes -#> 2024-05-29 18:54:57.874131 INFO::Fitting model to feature number 6, Atopobium -#> 2024-05-29 18:54:57.878924 INFO::Fitting model to feature number 7, Bacteroides -#> 2024-05-29 18:54:57.883656 INFO::Fitting model to feature number 8, Barnesiella -#> 2024-05-29 18:54:57.888304 INFO::Fitting model to feature number 9, Bifidobacterium -#> 2024-05-29 18:54:57.893035 INFO::Fitting model to feature number 10, Bilophila -#> 2024-05-29 18:54:57.897795 INFO::Fitting model to feature number 11, Blautia -#> 2024-05-29 18:54:57.902501 INFO::Fitting model to feature number 12, Butyricicoccus -#> 2024-05-29 18:54:57.907316 INFO::Fitting model to feature number 13, CAG.352 -#> 2024-05-29 18:54:57.912162 INFO::Fitting model to feature number 14, Campylobacter -#> 2024-05-29 18:54:57.917017 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group -#> 2024-05-29 18:54:57.921952 INFO::Fitting model to feature number 16, Clostridioides -#> 2024-05-29 18:54:57.926896 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1 -#> 2024-05-29 18:54:57.931841 INFO::Fitting model to feature number 18, Colidextribacter -#> 2024-05-29 18:54:57.936849 INFO::Fitting model to feature number 19, Collinsella -#> 2024-05-29 18:54:57.941874 INFO::Fitting model to feature number 20, Coprobacillus -#> 2024-05-29 18:54:57.946585 INFO::Fitting model to feature number 21, Coprococcus -#> 2024-05-29 18:54:57.951177 INFO::Fitting model to feature number 22, DTU089 -#> 2024-05-29 18:54:57.955792 INFO::Fitting model to feature number 23, Dialister -#> 2024-05-29 18:54:57.960646 INFO::Fitting model to feature number 24, Dorea -#> 2024-05-29 18:54:57.965628 INFO::Fitting model to feature number 25, Eggerthella -#> 2024-05-29 18:54:57.970688 INFO::Fitting model to feature number 26, Eisenbergiella -#> 2024-05-29 18:54:57.975654 INFO::Fitting model to feature number 27, Enterococcus -#> 2024-05-29 18:54:57.980691 INFO::Fitting model to feature number 28, Erysipelatoclostridium -#> 2024-05-29 18:54:57.985566 INFO::Fitting model to feature number 29, Erysipelotrichaceae.UCG.003 -#> 2024-05-29 18:54:57.990294 INFO::Fitting model to feature number 30, Escherichia.Shigella -#> 2024-05-29 18:54:57.995159 INFO::Fitting model to feature number 31, Faecalibacterium -#> 2024-05-29 18:54:57.999966 INFO::Fitting model to feature number 32, Family.XIII.AD3011.group -#> 2024-05-29 18:54:58.004654 INFO::Fitting model to feature number 33, Flavonifractor -#> 2024-05-29 18:54:58.00926 INFO::Fitting model to feature number 34, Fusicatenibacter -#> 2024-05-29 18:54:58.013871 INFO::Fitting model to feature number 35, Fusobacterium -#> 2024-05-29 18:54:58.01856 INFO::Fitting model to feature number 36, Gemella -#> 2024-05-29 18:54:58.023221 INFO::Fitting model to feature number 37, Granulicatella -#> 2024-05-29 18:54:58.027901 INFO::Fitting model to feature number 38, Haemophilus -#> 2024-05-29 18:54:58.032701 INFO::Fitting model to feature number 39, Holdemania -#> 2024-05-29 18:54:58.038824 INFO::Fitting model to feature number 40, Hungatella -#> 2024-05-29 18:54:58.045178 INFO::Fitting model to feature number 41, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis. -#> 2024-05-29 18:54:58.051616 INFO::Fitting model to feature number 42, Intestinibacter -#> 2024-05-29 18:54:58.058229 INFO::Fitting model to feature number 43, Intestinimonas -#> 2024-05-29 18:54:58.064884 INFO::Fitting model to feature number 44, Klebsiella -#> 2024-05-29 18:54:58.071465 INFO::Fitting model to feature number 45, Lachnoclostridium -#> 2024-05-29 18:54:58.086788 INFO::Fitting model to feature number 46, Lachnospira -#> 2024-05-29 18:54:58.091981 INFO::Fitting model to feature number 47, Lachnospiraceae.FCS020.group -#> 2024-05-29 18:54:58.09698 INFO::Fitting model to feature number 48, Lachnospiraceae.ND3007.group -#> 2024-05-29 18:54:58.10178 INFO::Fitting model to feature number 49, Lachnospiraceae.NK4A136.group -#> 2024-05-29 18:54:58.106682 INFO::Fitting model to feature number 50, Lachnospiraceae.UCG.001 -#> 2024-05-29 18:54:58.111483 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.004 -#> 2024-05-29 18:54:58.116278 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.009 -#> 2024-05-29 18:54:58.12114 INFO::Fitting model to feature number 53, Lachnospiraceae.UCG.010 -#> 2024-05-29 18:54:58.125859 INFO::Fitting model to feature number 54, Lactobacillus -#> 2024-05-29 18:54:58.130578 INFO::Fitting model to feature number 55, Lactococcus -#> 2024-05-29 18:54:58.135386 INFO::Fitting model to feature number 56, Mannheimia -#> 2024-05-29 18:54:58.140217 INFO::Fitting model to feature number 57, Megasphaera -#> 2024-05-29 18:54:58.145273 INFO::Fitting model to feature number 58, Monoglobus -#> 2024-05-29 18:54:58.150194 INFO::Fitting model to feature number 59, Neisseria -#> 2024-05-29 18:54:58.154996 INFO::Fitting model to feature number 60, Odoribacter -#> 2024-05-29 18:54:58.159687 INFO::Fitting model to feature number 61, Oscillibacter -#> 2024-05-29 18:54:58.164315 INFO::Fitting model to feature number 62, Oscillospira -#> 2024-05-29 18:54:58.16893 INFO::Fitting model to feature number 63, Parabacteroides -#> 2024-05-29 18:54:58.173518 INFO::Fitting model to feature number 64, Parasutterella -#> 2024-05-29 18:54:58.178206 INFO::Fitting model to feature number 65, Prevotella -#> 2024-05-29 18:54:58.182836 INFO::Fitting model to feature number 66, Pseudomonas -#> 2024-05-29 18:54:58.187421 INFO::Fitting model to feature number 67, Romboutsia -#> 2024-05-29 18:54:58.192134 INFO::Fitting model to feature number 68, Roseburia -#> 2024-05-29 18:54:58.196881 INFO::Fitting model to feature number 69, Rothia -#> 2024-05-29 18:54:58.201602 INFO::Fitting model to feature number 70, Ruminococcus -#> 2024-05-29 18:54:58.206331 INFO::Fitting model to feature number 71, Sellimonas -#> 2024-05-29 18:54:58.21103 INFO::Fitting model to feature number 72, Solobacterium -#> 2024-05-29 18:54:58.215667 INFO::Fitting model to feature number 73, Staphylococcus -#> 2024-05-29 18:54:58.220273 INFO::Fitting model to feature number 74, Streptococcus -#> 2024-05-29 18:54:58.224902 INFO::Fitting model to feature number 75, Subdoligranulum -#> 2024-05-29 18:54:58.229414 INFO::Fitting model to feature number 76, Sutterella -#> 2024-05-29 18:54:58.234368 INFO::Fitting model to feature number 77, Terrisporobacter -#> 2024-05-29 18:54:58.239767 INFO::Fitting model to feature number 78, Turicibacter -#> 2024-05-29 18:54:58.244613 INFO::Fitting model to feature number 79, Tuzzerella -#> 2024-05-29 18:54:58.249351 INFO::Fitting model to feature number 80, Tyzzerella -#> 2024-05-29 18:54:58.254018 INFO::Fitting model to feature number 81, UBA1819 -#> 2024-05-29 18:54:58.258654 INFO::Fitting model to feature number 82, UCG.002 -#> 2024-05-29 18:54:58.263248 INFO::Fitting model to feature number 83, UCG.003 -#> 2024-05-29 18:54:58.267733 INFO::Fitting model to feature number 84, UCG.005 -#> 2024-05-29 18:54:58.272211 INFO::Fitting model to feature number 85, Veillonella -#> 2024-05-29 18:54:58.276748 INFO::Fitting model to feature number 86, X.Clostridium..innocuum.group -#> 2024-05-29 18:54:58.281335 INFO::Fitting model to feature number 87, X.Eubacterium..eligens.group -#> 2024-05-29 18:54:58.285896 INFO::Fitting model to feature number 88, X.Eubacterium..fissicatena.group -#> 2024-05-29 18:54:58.299121 INFO::Fitting model to feature number 89, X.Eubacterium..hallii.group -#> 2024-05-29 18:54:58.304008 INFO::Fitting model to feature number 90, X.Eubacterium..siraeum.group -#> 2024-05-29 18:54:58.308665 INFO::Fitting model to feature number 91, X.Eubacterium..ventriosum.group -#> 2024-05-29 18:54:58.313264 INFO::Fitting model to feature number 92, X.Eubacterium..xylanophilum.group -#> 2024-05-29 18:54:58.317902 INFO::Fitting model to feature number 93, X.Ruminococcus..gauvreauii.group -#> 2024-05-29 18:54:58.322478 INFO::Fitting model to feature number 94, X.Ruminococcus..gnavus.group -#> 2024-05-29 18:54:58.327147 INFO::Fitting model to feature number 95, X.Ruminococcus..torques.group -#> 2024-05-29 18:54:58.331767 INFO::Fitting model to feature number 96, unclassified.Chloroplast -#> 2024-05-29 18:54:58.336325 INFO::Fitting model to feature number 97, unclassified.Clostridia.UCG.014 -#> 2024-05-29 18:54:58.340909 INFO::Fitting model to feature number 98, unclassified.Clostridia -#> 2024-05-29 18:54:58.345454 INFO::Fitting model to feature number 99, unclassified.Clostridia.vadinBB60.group -#> 2024-05-29 18:54:58.350013 INFO::Fitting model to feature number 100, unclassified.Gastranaerophilales -#> 2024-05-29 18:54:58.354642 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae -#> 2024-05-29 18:54:58.359296 INFO::Fitting model to feature number 102, unclassified.Mitochondria -#> 2024-05-29 18:54:58.36384 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae -#> 2024-05-29 18:54:58.368451 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus -#> 2024-05-29 18:54:58.373099 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales -#> 2024-05-29 18:54:58.378084 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae -#> 2024-05-29 18:54:58.382897 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group -#> 2024-05-29 18:54:58.403183 INFO::Counting total values for each feature -#> 2024-05-29 18:54:58.409404 INFO::Writing filtered data to file /tmp/Rtmp59uwfg/maaslin17f73b0d49b9/features/filtered_data.tsv -#> 2024-05-29 18:54:58.62526 INFO::Writing filtered, normalized data to file /tmp/Rtmp59uwfg/maaslin17f73b0d49b9/features/filtered_data_norm.tsv -#> 2024-05-29 18:54:58.843555 INFO::Writing filtered, normalized, transformed data to file /tmp/Rtmp59uwfg/maaslin17f73b0d49b9/features/filtered_data_norm_transformed.tsv -#> 2024-05-29 18:54:59.202225 INFO::Writing residuals to file /tmp/Rtmp59uwfg/maaslin17f73b0d49b9/fits/residuals.rds -#> 2024-05-29 18:54:59.274287 INFO::Writing fitted values to file /tmp/Rtmp59uwfg/maaslin17f73b0d49b9/fits/fitted.rds -#> 2024-05-29 18:54:59.299379 INFO::Writing all results to file (ordered by increasing q-values): /tmp/Rtmp59uwfg/maaslin17f73b0d49b9/all_results.tsv -#> 2024-05-29 18:54:59.301404 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/Rtmp59uwfg/maaslin17f73b0d49b9/significant_results.tsv +#> 2024-05-29 19:24:25.690366 INFO::Writing function arguments to log file +#> 2024-05-29 19:24:25.705246 INFO::Verifying options selected are valid +#> 2024-05-29 19:24:25.733716 INFO::Determining format of input files +#> 2024-05-29 19:24:25.735584 INFO::Input format is data samples as rows and metadata samples as rows +#> 2024-05-29 19:24:25.750988 INFO::Formula for fixed effects: expr ~ delivery_mode +#> 2024-05-29 19:24:25.75208 INFO::Filter data based on min abundance and min prevalence +#> 2024-05-29 19:24:25.752573 INFO::Total samples in data: 3184 +#> 2024-05-29 19:24:25.753039 INFO::Min samples required with min abundance for a feature not to be filtered: 318.400000 +#> 2024-05-29 19:24:25.786399 INFO::Total filtered features: 564 +#> 2024-05-29 19:24:25.78754 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 +#> 2024-05-29 19:24:25.795631 INFO::Total filtered features with variance filtering: 0 +#> 2024-05-29 19:24:25.796263 INFO::Filtered feature names from variance filtering: +#> 2024-05-29 19:24:25.796727 INFO::Running selected normalization method: TSS +#> 2024-05-29 19:24:25.860186 INFO::Applying z-score to standardize continuous metadata +#> 2024-05-29 19:24:25.868514 INFO::Running selected transform method: LOG +#> 2024-05-29 19:24:25.942575 INFO::Running selected analysis method: LM +#> 2024-05-29 19:24:25.948629 INFO::Fitting model to feature number 1, Actinomyces +#> 2024-05-29 19:24:25.979003 INFO::Fitting model to feature number 2, Agathobacter +#> 2024-05-29 19:24:25.983799 INFO::Fitting model to feature number 3, Akkermansia +#> 2024-05-29 19:24:25.988428 INFO::Fitting model to feature number 4, Alistipes +#> 2024-05-29 19:24:25.992916 INFO::Fitting model to feature number 5, Anaerostipes +#> 2024-05-29 19:24:25.99738 INFO::Fitting model to feature number 6, Atopobium +#> 2024-05-29 19:24:26.001847 INFO::Fitting model to feature number 7, Bacteroides +#> 2024-05-29 19:24:26.006279 INFO::Fitting model to feature number 8, Barnesiella +#> 2024-05-29 19:24:26.010787 INFO::Fitting model to feature number 9, Bifidobacterium +#> 2024-05-29 19:24:26.015297 INFO::Fitting model to feature number 10, Bilophila +#> 2024-05-29 19:24:26.01981 INFO::Fitting model to feature number 11, Blautia +#> 2024-05-29 19:24:26.024316 INFO::Fitting model to feature number 12, Butyricicoccus +#> 2024-05-29 19:24:26.02882 INFO::Fitting model to feature number 13, CAG.352 +#> 2024-05-29 19:24:26.03335 INFO::Fitting model to feature number 14, Campylobacter +#> 2024-05-29 19:24:26.037838 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group +#> 2024-05-29 19:24:26.042363 INFO::Fitting model to feature number 16, Clostridioides +#> 2024-05-29 19:24:26.046896 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1 +#> 2024-05-29 19:24:26.051427 INFO::Fitting model to feature number 18, Colidextribacter +#> 2024-05-29 19:24:26.055922 INFO::Fitting model to feature number 19, Collinsella +#> 2024-05-29 19:24:26.060429 INFO::Fitting model to feature number 20, Coprobacillus +#> 2024-05-29 19:24:26.064972 INFO::Fitting model to feature number 21, Coprococcus +#> 2024-05-29 19:24:26.069502 INFO::Fitting model to feature number 22, DTU089 +#> 2024-05-29 19:24:26.073978 INFO::Fitting model to feature number 23, Dialister +#> 2024-05-29 19:24:26.078469 INFO::Fitting model to feature number 24, Dorea +#> 2024-05-29 19:24:26.082997 INFO::Fitting model to feature number 25, Eggerthella +#> 2024-05-29 19:24:26.08753 INFO::Fitting model to feature number 26, Eisenbergiella +#> 2024-05-29 19:24:26.092058 INFO::Fitting model to feature number 27, Enterococcus +#> 2024-05-29 19:24:26.096586 INFO::Fitting model to feature number 28, Erysipelatoclostridium +#> 2024-05-29 19:24:26.101109 INFO::Fitting model to feature number 29, Erysipelotrichaceae.UCG.003 +#> 2024-05-29 19:24:26.105609 INFO::Fitting model to feature number 30, Escherichia.Shigella +#> 2024-05-29 19:24:26.110118 INFO::Fitting model to feature number 31, Faecalibacterium +#> 2024-05-29 19:24:26.114599 INFO::Fitting model to feature number 32, Family.XIII.AD3011.group +#> 2024-05-29 19:24:26.119081 INFO::Fitting model to feature number 33, Flavonifractor +#> 2024-05-29 19:24:26.12356 INFO::Fitting model to feature number 34, Fusicatenibacter +#> 2024-05-29 19:24:26.128036 INFO::Fitting model to feature number 35, Fusobacterium +#> 2024-05-29 19:24:26.132512 INFO::Fitting model to feature number 36, Gemella +#> 2024-05-29 19:24:26.136961 INFO::Fitting model to feature number 37, Granulicatella +#> 2024-05-29 19:24:26.141517 INFO::Fitting model to feature number 38, Haemophilus +#> 2024-05-29 19:24:26.145974 INFO::Fitting model to feature number 39, Holdemania +#> 2024-05-29 19:24:26.150461 INFO::Fitting model to feature number 40, Hungatella +#> 2024-05-29 19:24:26.155035 INFO::Fitting model to feature number 41, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis. +#> 2024-05-29 19:24:26.160233 INFO::Fitting model to feature number 42, Intestinibacter +#> 2024-05-29 19:24:26.164831 INFO::Fitting model to feature number 43, Intestinimonas +#> 2024-05-29 19:24:26.169403 INFO::Fitting model to feature number 44, Klebsiella +#> 2024-05-29 19:24:26.173961 INFO::Fitting model to feature number 45, Lachnoclostridium +#> 2024-05-29 19:24:26.187146 INFO::Fitting model to feature number 46, Lachnospira +#> 2024-05-29 19:24:26.191819 INFO::Fitting model to feature number 47, Lachnospiraceae.FCS020.group +#> 2024-05-29 19:24:26.196344 INFO::Fitting model to feature number 48, Lachnospiraceae.ND3007.group +#> 2024-05-29 19:24:26.200874 INFO::Fitting model to feature number 49, Lachnospiraceae.NK4A136.group +#> 2024-05-29 19:24:26.205418 INFO::Fitting model to feature number 50, Lachnospiraceae.UCG.001 +#> 2024-05-29 19:24:26.20992 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.004 +#> 2024-05-29 19:24:26.214427 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.009 +#> 2024-05-29 19:24:26.218975 INFO::Fitting model to feature number 53, Lachnospiraceae.UCG.010 +#> 2024-05-29 19:24:26.223496 INFO::Fitting model to feature number 54, Lactobacillus +#> 2024-05-29 19:24:26.228008 INFO::Fitting model to feature number 55, Lactococcus +#> 2024-05-29 19:24:26.232537 INFO::Fitting model to feature number 56, Mannheimia +#> 2024-05-29 19:24:26.237012 INFO::Fitting model to feature number 57, Megasphaera +#> 2024-05-29 19:24:26.241517 INFO::Fitting model to feature number 58, Monoglobus +#> 2024-05-29 19:24:26.246049 INFO::Fitting model to feature number 59, Neisseria +#> 2024-05-29 19:24:26.250579 INFO::Fitting model to feature number 60, Odoribacter +#> 2024-05-29 19:24:26.255095 INFO::Fitting model to feature number 61, Oscillibacter +#> 2024-05-29 19:24:26.259666 INFO::Fitting model to feature number 62, Oscillospira +#> 2024-05-29 19:24:26.264181 INFO::Fitting model to feature number 63, Parabacteroides +#> 2024-05-29 19:24:26.268688 INFO::Fitting model to feature number 64, Parasutterella +#> 2024-05-29 19:24:26.273212 INFO::Fitting model to feature number 65, Prevotella +#> 2024-05-29 19:24:26.277699 INFO::Fitting model to feature number 66, Pseudomonas +#> 2024-05-29 19:24:26.282174 INFO::Fitting model to feature number 67, Romboutsia +#> 2024-05-29 19:24:26.286703 INFO::Fitting model to feature number 68, Roseburia +#> 2024-05-29 19:24:26.291175 INFO::Fitting model to feature number 69, Rothia +#> 2024-05-29 19:24:26.295656 INFO::Fitting model to feature number 70, Ruminococcus +#> 2024-05-29 19:24:26.300152 INFO::Fitting model to feature number 71, Sellimonas +#> 2024-05-29 19:24:26.304675 INFO::Fitting model to feature number 72, Solobacterium +#> 2024-05-29 19:24:26.309137 INFO::Fitting model to feature number 73, Staphylococcus +#> 2024-05-29 19:24:26.313603 INFO::Fitting model to feature number 74, Streptococcus +#> 2024-05-29 19:24:26.31805 INFO::Fitting model to feature number 75, Subdoligranulum +#> 2024-05-29 19:24:26.322621 INFO::Fitting model to feature number 76, Sutterella +#> 2024-05-29 19:24:26.327203 INFO::Fitting model to feature number 77, Terrisporobacter +#> 2024-05-29 19:24:26.331767 INFO::Fitting model to feature number 78, Turicibacter +#> 2024-05-29 19:24:26.336348 INFO::Fitting model to feature number 79, Tuzzerella +#> 2024-05-29 19:24:26.340919 INFO::Fitting model to feature number 80, Tyzzerella +#> 2024-05-29 19:24:26.345466 INFO::Fitting model to feature number 81, UBA1819 +#> 2024-05-29 19:24:26.350018 INFO::Fitting model to feature number 82, UCG.002 +#> 2024-05-29 19:24:26.354594 INFO::Fitting model to feature number 83, UCG.003 +#> 2024-05-29 19:24:26.359101 INFO::Fitting model to feature number 84, UCG.005 +#> 2024-05-29 19:24:26.363616 INFO::Fitting model to feature number 85, Veillonella +#> 2024-05-29 19:24:26.368161 INFO::Fitting model to feature number 86, X.Clostridium..innocuum.group +#> 2024-05-29 19:24:26.372703 INFO::Fitting model to feature number 87, X.Eubacterium..eligens.group +#> 2024-05-29 19:24:26.377274 INFO::Fitting model to feature number 88, X.Eubacterium..fissicatena.group +#> 2024-05-29 19:24:26.390749 INFO::Fitting model to feature number 89, X.Eubacterium..hallii.group +#> 2024-05-29 19:24:26.395689 INFO::Fitting model to feature number 90, X.Eubacterium..siraeum.group +#> 2024-05-29 19:24:26.400324 INFO::Fitting model to feature number 91, X.Eubacterium..ventriosum.group +#> 2024-05-29 19:24:26.404863 INFO::Fitting model to feature number 92, X.Eubacterium..xylanophilum.group +#> 2024-05-29 19:24:26.409348 INFO::Fitting model to feature number 93, X.Ruminococcus..gauvreauii.group +#> 2024-05-29 19:24:26.413847 INFO::Fitting model to feature number 94, X.Ruminococcus..gnavus.group +#> 2024-05-29 19:24:26.418364 INFO::Fitting model to feature number 95, X.Ruminococcus..torques.group +#> 2024-05-29 19:24:26.422974 INFO::Fitting model to feature number 96, unclassified.Chloroplast +#> 2024-05-29 19:24:26.427526 INFO::Fitting model to feature number 97, unclassified.Clostridia.UCG.014 +#> 2024-05-29 19:24:26.432042 INFO::Fitting model to feature number 98, unclassified.Clostridia +#> 2024-05-29 19:24:26.436579 INFO::Fitting model to feature number 99, unclassified.Clostridia.vadinBB60.group +#> 2024-05-29 19:24:26.441093 INFO::Fitting model to feature number 100, unclassified.Gastranaerophilales +#> 2024-05-29 19:24:26.445596 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae +#> 2024-05-29 19:24:26.450059 INFO::Fitting model to feature number 102, unclassified.Mitochondria +#> 2024-05-29 19:24:26.454511 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae +#> 2024-05-29 19:24:26.459109 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus +#> 2024-05-29 19:24:26.463578 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales +#> 2024-05-29 19:24:26.468143 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae +#> 2024-05-29 19:24:26.472611 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group +#> 2024-05-29 19:24:26.491841 INFO::Counting total values for each feature +#> 2024-05-29 19:24:26.497712 INFO::Writing filtered data to file /tmp/RtmpLeA4YZ/maaslin181724b08cba/features/filtered_data.tsv +#> 2024-05-29 19:24:26.713719 INFO::Writing filtered, normalized data to file /tmp/RtmpLeA4YZ/maaslin181724b08cba/features/filtered_data_norm.tsv +#> 2024-05-29 19:24:26.933167 INFO::Writing filtered, normalized, transformed data to file /tmp/RtmpLeA4YZ/maaslin181724b08cba/features/filtered_data_norm_transformed.tsv +#> 2024-05-29 19:24:27.291177 INFO::Writing residuals to file /tmp/RtmpLeA4YZ/maaslin181724b08cba/fits/residuals.rds +#> 2024-05-29 19:24:27.362971 INFO::Writing fitted values to file /tmp/RtmpLeA4YZ/maaslin181724b08cba/fits/fitted.rds +#> 2024-05-29 19:24:27.388593 INFO::Writing all results to file (ordered by increasing q-values): /tmp/RtmpLeA4YZ/maaslin181724b08cba/all_results.tsv +#> 2024-05-29 19:24:27.390475 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/RtmpLeA4YZ/maaslin181724b08cba/significant_results.tsv