MaAsLin2 User Manual

MaAsLin2 is the next generation of MaAsLin (Microbiome Multivariable Association with Linear Models).

MaAsLin2 is comprehensive R package for efficiently determining multivariable association between clinical metadata and microbial meta-omics features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, along with a variety of filtering, normalization, and transform methods.

If you use the MaAsLin2 software, please cite our manuscript:

Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, Tickle TL, Weingart G, Ren B, Schwager EH, Chatterjee S, Thompson KN, Wilkinson JE, Subramanian A, Lu Y, Waldron L, Paulson JN, Franzosa EA, Bravo HC, Huttenhower C (2021). Multivariable Association Discovery in Population-scale Meta-omics Studies. PLoS Computational Biology, 17(11):e1009442.

Check out the MaAsLin 2 tutorial for an overview of analysis options.

If you have questions, please direct it to :
MaAsLin2 Forum
Google Groups (Read only)

Description
Requirements
Installation
How to Run
Visualization
Troubleshooting

Description

MaAsLin2 finds associations between microbiome multi-omics features and complex metadata in population-scale epidemiological studies. The software includes multiple analysis methods (with support for multiple covariates and repeated measures), filtering, normalization, and transform options to customize analysis for your specific study.

Requirements

MaAsLin2 is an R package that can be run on the command line or as an R function.

Installation

MaAsLin2 can be run from the command line or as an R function. If only running from the command line, you do not need to install the MaAsLin2 package but you will need to install the MaAsLin2 dependencies.

From command line

Download the source: MaAsLin2.tar.gz
Decompress the download:
- $ tar xzvf maaslin2.tar.gz
Install the Bioconductor dependencies edgeR and metagenomeSeq.
Install the CRAN dependencies:
- $ R -q -e "install.packages(c('lmerTest','pbapply','car','dplyr','vegan','chemometrics','ggplot2','pheatmap','hash','logging','data.table','glmmTMB','MASS','cplm','pscl'), repos='http://cran.r-project.org')"
Install the MaAsLin2 package (only r,equired if running as an R function):
- $ R CMD INSTALL maaslin2

From R

Install Bioconductor and then install Maaslin2

if(!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("Maaslin2")

How to Run

MaAsLin2 can be run from the command line or as an R function. Both methods require the same arguments, have the same options, and use the same default settings.

Input Files

MaAsLin2 requires two input files.

Data (or features) file
- This file is tab-delimited.
- Formatted with features as columns and samples as rows.
- The transpose of this format is also okay.
- Possible features in this file include taxonomy or genes.
Metadata file
- This file is tab-delimited.
- Formatted with features as columns and samples as rows.
- The transpose of this format is also okay.
- Possible metadata in this file include gender or age.

The data file can contain samples not included in the metadata file (along with the reverse case). For both cases, those samples not included in both files will be removed from the analysis. Also the samples do not need to be in the same order in the two files.

NOTE: If running MaAsLin2 as a function, the data and metadata inputs can be of type data.frame instead of a path to a file.

Output Files

MaAsLin2 generates two types of output files: data and visualization.

Data output files
- all_results.tsv
  - This includes the same data as the data.frame returned.
  - This file contains all results ordered by increasing q-value.
  - The first columns are the metadata and feature names.
  - The next two columns are the value and coefficient from the model.
  - The next column is the standard deviation from the model.
  - The N column is the total number of data points.
  - The N.not.zero column is the total of non-zero data points.
  - The pvalue from the calculation is the second to last column.
  - The qvalue is computed with p.adjust with the correction method.
- significant_results.tsv
  - This file is a subset of the results in the first file.
  - It only includes associations with q-values <= to the threshold.
- ``features```
  - This folder includes the filtered, normalized, and transformed versions of the input feature table.
  - These steps are performed sequentially in the above order.
  - If an option is set such that a step does not change the data, the resulting table will still be output.
- models.rds
  - This file contains a list with every model fit object.
  - It will only be generated if save_models is set to TRUE.
- residuals.rds
  - This file contains a data frame with residuals for each feature.
- fitted.rds
  - This file contains a data frame with fitted values for each feature.
- ranef.rds
  - This file contains a data frame with extracted random effects for each feature (when random effects are specified).
- maaslin2.log
  - This file contains all log information for the run.
  - It includes all settings, warnings, errors, and steps run.
Visualization output files
- heatmap.pdf
  - This file contains a heatmap of the significant associations.
- [a-z/0-9]+.pdf
  - A plot is generated for each significant association.
  - Scatter plots are used for continuous metadata.
  - Box plots are for categorical data.
  - Data points plotted are after filtering but prior to normalization and transform.

Run a Demo

Example input files can be found in the inst/extdata folder of the MaAsLin2 source. The files provided were generated from the HMP2 data which can be downloaded from https://ibdmdb.org/ .

HMP2_taxonomy.tsv: is a tab-demilited file with species as columns and samples as rows. It is a subset of the taxonomy file so it just includes the species abundances for all samples.

HMP2_metadata.tsv: is a tab-delimited file with samples as rows and metadata as columns. It is a subset of the metadata file so that it just includes some of the fields.

Command line

$ Maaslin2.R --fixed_effects="diagnosis,dysbiosisnonIBD,dysbiosisUC,dysbiosisCD,antibiotics,age" --random_effects="site,subject" --standardize=FALSE inst/extdata/HMP2_taxonomy.tsv inst/extdata/HMP2_metadata.tsv demo_output

Make sure to provide the full path to the MaAsLin2 executable (ie ./R/Maaslin2.R).
In the demo command:
- HMP2_taxonomy.tsv is the path to your data (or features) file
- HMP2_metadata.tsv is the path to your metadata file
- demo_output is the path to the folder to write the output

In R

library(Maaslin2)
input_data <- system.file(
    'extdata','HMP2_taxonomy.tsv', package="Maaslin2")
input_metadata <-system.file(
    'extdata','HMP2_metadata.tsv', package="Maaslin2")
fit_data <- Maaslin2(
    input_data, input_metadata, 'demo_output',
    fixed_effects = c('diagnosis', 'dysbiosisnonIBD','dysbiosisUC','dysbiosisCD', 'antibiotics', 'age'),
    random_effects = c('site', 'subject'),
    reference = "diagnosis,nonIBD",
    standardize = FALSE)

## [1] "Creating output folder"
## [1] "Creating output feature tables folder"
## [1] "Creating output fits folder"
## [1] "Creating output figures folder"
## 2026-05-29 08:54:16.296111 INFO::Writing function arguments to log file
## 2026-05-29 08:54:16.396223 INFO::Verifying options selected are valid
## 2026-05-29 08:54:16.417471 INFO::Determining format of input files
## 2026-05-29 08:54:16.41841 INFO::Input format is data samples as rows and metadata samples as rows
## 2026-05-29 08:54:16.422302 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2026-05-29 08:54:16.423159 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2026-05-29 08:54:16.424781 INFO::Filter data based on min abundance and min prevalence
## 2026-05-29 08:54:16.425281 INFO::Total samples in data: 1595
## 2026-05-29 08:54:16.425754 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2026-05-29 08:54:16.430282 INFO::Total filtered features: 0
## 2026-05-29 08:54:16.431305 INFO::Filtered feature names from abundance and prevalence filtering:
## 2026-05-29 08:54:16.439856 INFO::Total filtered features with variance filtering: 0
## 2026-05-29 08:54:16.44074 INFO::Filtered feature names from variance filtering:
## 2026-05-29 08:54:16.441278 INFO::Running selected normalization method: TSS
## 2026-05-29 08:54:17.292157 INFO::Bypass z-score application to metadata
## 2026-05-29 08:54:17.293056 INFO::Running selected transform method: LOG
## 2026-05-29 08:54:17.315894 INFO::Running selected analysis method: LM
## 2026-05-29 08:54:17.537203 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:18.157591 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2026-05-29 08:54:18.254809 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2026-05-29 08:54:18.345387 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:18.44244 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2026-05-29 08:54:18.541893 INFO::Fitting model to feature number 6, Bacteroides.caccae

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:18.646645 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2026-05-29 08:54:18.740654 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2026-05-29 08:54:18.840968 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2026-05-29 08:54:18.941875 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2026-05-29 08:54:19.039393 INFO::Fitting model to feature number 11, Bacteroides.finegoldii

## boundary (singular) fit: see help('isSingular')

## Feature Bacteroides.finegoldii : simpleWarning: Model failed to converge with 1 negative eigenvalue: -7.9e+01

## 2026-05-29 08:54:19.113963 WARNING::Fitting problem for feature 11 a warning was issued

## boundary (singular) fit: see help('isSingular')

## Warning: Model failed to converge with 1 negative eigenvalue: -7.9e+01

## 2026-05-29 08:54:19.20961 INFO::Fitting model to feature number 12, Bacteroides.fragilis

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:19.298244 INFO::Fitting model to feature number 13, Bacteroides.intestinalis

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:19.399993 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2026-05-29 08:54:19.490165 INFO::Fitting model to feature number 15, Bacteroides.ovatus

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:19.57481 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2026-05-29 08:54:19.673002 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2026-05-29 08:54:19.763304 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:19.855815 INFO::Fitting model to feature number 19, Bacteroides.uniformis

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:19.944577 INFO::Fitting model to feature number 20, Bacteroides.vulgatus

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:20.032917 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:20.126133 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2026-05-29 08:54:20.214206 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2026-05-29 08:54:20.305732 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2026-05-29 08:54:20.404746 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2026-05-29 08:54:20.495543 INFO::Fitting model to feature number 26, Parabacteroides.distasonis

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:20.592333 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2026-05-29 08:54:20.684602 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2026-05-29 08:54:20.77811 INFO::Fitting model to feature number 29, Parabacteroides.unclassified

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:20.871276 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2026-05-29 08:54:20.965843 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2026-05-29 08:54:21.065377 INFO::Fitting model to feature number 32, Prevotella.copri

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:21.15501 INFO::Fitting model to feature number 33, Alistipes.finegoldii

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:21.242891 INFO::Fitting model to feature number 34, Alistipes.onderdonkii

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:21.342026 INFO::Fitting model to feature number 35, Alistipes.putredinis

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:21.433687 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2026-05-29 08:54:21.534328 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2026-05-29 08:54:21.623294 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2026-05-29 08:54:21.724965 INFO::Fitting model to feature number 39, Clostridium.bolteae

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:21.816424 INFO::Fitting model to feature number 40, Clostridium.citroniae

## boundary (singular) fit: see help('isSingular')

## Feature Clostridium.citroniae : simpleWarning: Model failed to converge with 1 negative eigenvalue: -3.4e+01

## 2026-05-29 08:54:21.895408 WARNING::Fitting problem for feature 40 a warning was issued

## boundary (singular) fit: see help('isSingular')

## Warning: Model failed to converge with 1 negative eigenvalue: -3.4e+01

## 2026-05-29 08:54:21.986091 INFO::Fitting model to feature number 41, Clostridium.clostridioforme

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:22.079074 INFO::Fitting model to feature number 42, Clostridium.hathewayi

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:22.167343 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2026-05-29 08:54:22.272207 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2026-05-29 08:54:22.361021 INFO::Fitting model to feature number 45, Clostridium.symbiosum

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:22.455353 INFO::Fitting model to feature number 46, Flavonifractor.plautii

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:22.55211 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2026-05-29 08:54:22.643455 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2026-05-29 08:54:22.752113 INFO::Fitting model to feature number 49, Eubacterium.rectale

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:22.847145 INFO::Fitting model to feature number 50, Eubacterium.siraeum

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:22.944086 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:23.033293 INFO::Fitting model to feature number 52, Eubacterium.ventriosum

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:23.121517 INFO::Fitting model to feature number 53, Ruminococcus.gnavus

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:23.218869 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2026-05-29 08:54:23.307972 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2026-05-29 08:54:23.619652 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2026-05-29 08:54:23.711582 INFO::Fitting model to feature number 57, Dorea.longicatena

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:23.800305 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:23.896618 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:24.005886 INFO::Fitting model to feature number 60, Roseburia.hominis

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:24.113003 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2026-05-29 08:54:24.199733 INFO::Fitting model to feature number 62, Roseburia.inulinivorans

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:24.287639 INFO::Fitting model to feature number 63, Roseburia.unclassified

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:24.376919 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2026-05-29 08:54:24.475226 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2026-05-29 08:54:24.576205 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2026-05-29 08:54:24.670376 INFO::Fitting model to feature number 67, Ruminococcus.bromii

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:24.758082 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2026-05-29 08:54:24.846978 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2026-05-29 08:54:24.947431 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:25.035627 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2026-05-29 08:54:25.122184 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2026-05-29 08:54:25.213373 INFO::Fitting model to feature number 73, Dialister.invisus

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:25.29802 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2026-05-29 08:54:25.39635 INFO::Fitting model to feature number 75, Veillonella.dispar

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:25.487351 INFO::Fitting model to feature number 76, Veillonella.parvula

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:25.574022 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2026-05-29 08:54:25.662458 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2026-05-29 08:54:25.76278 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2026-05-29 08:54:25.851277 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2026-05-29 08:54:25.945084 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2026-05-29 08:54:26.043427 INFO::Fitting model to feature number 82, Escherichia.coli
## 2026-05-29 08:54:26.13693 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2026-05-29 08:54:26.229686 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:26.314336 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae

## boundary (singular) fit: see help('isSingular')

## 2026-05-29 08:54:26.4038 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2026-05-29 08:54:26.497284 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2026-05-29 08:54:26.623292 INFO::Counting total values for each feature
## 2026-05-29 08:54:26.643302 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2026-05-29 08:54:26.704719 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2026-05-29 08:54:26.766046 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2026-05-29 08:54:26.860173 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2026-05-29 08:54:26.90225 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2026-05-29 08:54:26.925659 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2026-05-29 08:54:26.929513 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2026-05-29 08:54:26.932739 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): demo_output/significant_results.tsv
## 2026-05-29 08:54:26.934232 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2026-05-29 08:54:27.33509 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2026-05-29 08:54:27.339273 INFO::Plotting associations from most to least significant, grouped by metadata
## 2026-05-29 08:54:27.339904 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2026-05-29 08:54:27.340945 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii

## 2026-05-29 08:54:27.639111 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified

## 2026-05-29 08:54:27.890543 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis

## 2026-05-29 08:54:28.130581 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale

## 2026-05-29 08:54:28.368505 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus

## 2026-05-29 08:54:28.607598 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus

## 2026-05-29 08:54:28.848341 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum

## 2026-05-29 08:54:29.093881 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified

## 2026-05-29 08:54:29.341599 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans

## 2026-05-29 08:54:29.582605 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis

## 2026-05-29 08:54:29.825895 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron

## 2026-05-29 08:54:30.066906 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis

## 2026-05-29 08:54:30.306455 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis

## 2026-05-29 08:54:30.541395 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei

## 2026-05-29 08:54:30.848273 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii

## 2026-05-29 08:54:31.112586 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens

## 2026-05-29 08:54:31.358315 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum

## 2026-05-29 08:54:31.601611 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena

## 2026-05-29 08:54:31.841506 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae

## 2026-05-29 08:54:32.088648 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-05-29 08:54:32.330374 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli

## 2026-05-29 08:54:32.57271 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae

## 2026-05-29 08:54:32.82709 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified

## 2026-05-29 08:54:33.067734 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii

## 2026-05-29 08:54:33.306441 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens

## 2026-05-29 08:54:33.546545 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris

## 2026-05-29 08:54:33.799505 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes

## 2026-05-29 08:54:34.041076 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis

## 2026-05-29 08:54:34.284971 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii

## 2026-05-29 08:54:34.538326 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii

## 2026-05-29 08:54:34.779131 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis

## 2026-05-29 08:54:35.064923 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara

## 2026-05-29 08:54:35.326669 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum

## 2026-05-29 08:54:35.575183 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae

## 2026-05-29 08:54:35.824939 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified

## 2026-05-29 08:54:36.088024 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens

## 2026-05-29 08:54:36.338531 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus

## 2026-05-29 08:54:36.589213 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme

## 2026-05-29 08:54:36.838266 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii

## 2026-05-29 08:54:37.090351 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii

## 2026-05-29 08:54:37.343071 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum

## 2026-05-29 08:54:37.605286 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris

## 2026-05-29 08:54:37.857812 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47

## 2026-05-29 08:54:38.106308 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus

## 2026-05-29 08:54:38.373351 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii

## 2026-05-29 08:54:38.625045 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis

## 2026-05-29 08:54:38.873619 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified

## 2026-05-29 08:54:39.141278 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques

## 2026-05-29 08:54:39.42783 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified

## 2026-05-29 08:54:39.69676 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus

## 2026-05-29 08:54:39.949718 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis

## 2026-05-29 08:54:40.213691 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified

## 2026-05-29 08:54:40.483787 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified

## 2026-05-29 08:54:40.753152 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis

## 2026-05-29 08:54:41.008922 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis

## 2026-05-29 08:54:41.267139 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31

## 2026-05-29 08:54:41.521636 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae

## 2026-05-29 08:54:41.782236 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8

## 2026-05-29 08:54:42.043037 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae

## 2026-05-29 08:54:42.299551 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii

## 2026-05-29 08:54:42.554708 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii

## 2026-05-29 08:54:42.837171 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum

## 2026-05-29 08:54:43.092935 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA

## 2026-05-29 08:54:45.797561 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2026-05-29 08:54:45.799242 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified

## 2026-05-29 08:54:46.049854 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii

## 2026-05-29 08:54:46.326158 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae

## 2026-05-29 08:54:46.603674 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified

## 2026-05-29 08:54:46.879074 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis

## 2026-05-29 08:54:47.165519 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum

## 2026-05-29 08:54:47.455946 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus

## 2026-05-29 08:54:47.721641 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis

## 2026-05-29 08:54:48.003045 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii

## 2026-05-29 08:54:48.292443 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale

## 2026-05-29 08:54:48.574407 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis

## 2026-05-29 08:54:48.852023 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis

## 2026-05-29 08:54:49.456598 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-05-29 08:54:49.69569 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii

## 2026-05-29 08:54:49.933737 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens

## 2026-05-29 08:54:50.16975 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris

## 2026-05-29 08:54:50.405564 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii

## 2026-05-29 08:54:50.644848 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis

## 2026-05-29 08:54:50.878995 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum

## 2026-05-29 08:54:51.115004 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus

## 2026-05-29 08:54:51.35086 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii

## 2026-05-29 08:54:51.59076 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii

## 2026-05-29 08:54:51.825711 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae

## 2026-05-29 08:54:52.064293 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus

## 2026-05-29 08:54:52.306057 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum

## 2026-05-29 08:54:52.539662 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae

## 2026-05-29 08:54:52.778404 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae

## 2026-05-29 08:54:53.011436 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum

## 2026-05-29 08:54:53.242384 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis

## 2026-05-29 08:54:53.475822 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii

## 2026-05-29 08:54:53.769777 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques

## 2026-05-29 08:54:54.017394 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8

## 2026-05-29 08:54:54.276544 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum

## 2026-05-29 08:54:54.521844 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum

## 2026-05-29 08:54:54.778112 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis

## 2026-05-29 08:54:55.025744 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens

## 2026-05-29 08:54:55.271714 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi

## 2026-05-29 08:54:55.535208 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified

## 2026-05-29 08:54:55.787685 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens

## 2026-05-29 08:54:56.040246 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus

## 2026-05-29 08:54:56.288418 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae

## 2026-05-29 08:54:56.555941 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus

## 2026-05-29 08:54:56.813731 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris

## 2026-05-29 08:54:57.064797 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47

## 2026-05-29 08:54:59.6472 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2026-05-29 08:54:59.648914 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii

## 2026-05-29 08:54:59.881638 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale

## 2026-05-29 08:55:00.146443 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31

## 2026-05-29 08:55:00.409575 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis

## 2026-05-29 08:55:00.67979 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified

## 2026-05-29 08:55:00.941591 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-05-29 08:55:01.208729 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques

## 2026-05-29 08:55:01.471944 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum

## 2026-05-29 08:55:01.747694 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus

## 2026-05-29 08:55:02.016455 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli

## 2026-05-29 08:55:02.276045 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum

## 2026-05-29 08:55:02.544041 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified

## 2026-05-29 08:55:02.824788 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis

## 2026-05-29 08:55:03.134525 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens

## 2026-05-29 08:55:03.41352 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae

## 2026-05-29 08:55:03.709162 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii

## 2026-05-29 08:55:03.972405 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus

## 2026-05-29 08:55:04.235569 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified

## 2026-05-29 08:55:04.520321 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis

## 2026-05-29 08:55:04.791144 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii

## 2026-05-29 08:55:05.068738 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans

## 2026-05-29 08:55:05.374674 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii

## 2026-05-29 08:55:05.661138 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified

## 2026-05-29 08:55:05.952226 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii

## 2026-05-29 08:55:06.230859 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis

## 2026-05-29 08:55:06.527935 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri

## 2026-05-29 08:55:06.808918 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei

## 2026-05-29 08:55:07.099871 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis

## 2026-05-29 08:55:07.428305 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii

## 2026-05-29 08:55:10.194326 INFO::Plotting data for metadata number 4, antibiotics
## 2026-05-29 08:55:10.19604 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans

## 2026-05-29 08:55:10.443417 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis

## 2026-05-29 08:55:10.715157 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale

## 2026-05-29 08:55:10.995794 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus

## 2026-05-29 08:55:11.278601 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis

## 2026-05-29 08:55:11.548416 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena

## 2026-05-29 08:55:11.837297 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus

## 2026-05-29 08:55:12.108329 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii

## 2026-05-29 08:55:12.415286 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum

## 2026-05-29 08:55:12.706533 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae

## 2026-05-29 08:55:12.985604 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis

## 2026-05-29 08:55:13.258737 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii

## 2026-05-29 08:55:13.549322 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii

## 2026-05-29 08:55:13.826808 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified

## 2026-05-29 08:55:14.124707 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum

## 2026-05-29 08:55:14.400632 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-05-29 08:55:14.690409 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii

## 2026-05-29 08:55:14.96703 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31

## 2026-05-29 08:55:15.256053 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis

## 2026-05-29 08:55:15.516584 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii

## 2026-05-29 08:55:15.804357 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis

## 2026-05-29 08:55:16.102014 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens

## 2026-05-29 08:55:16.679818 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens

## 2026-05-29 08:55:16.907752 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron

## 2026-05-29 08:55:17.135925 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii

## 2026-05-29 08:55:17.366867 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae

## 2026-05-29 08:55:17.586263 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum

## 2026-05-29 08:55:17.810146 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques

## 2026-05-29 08:55:18.035903 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum

## 2026-05-29 08:55:18.264716 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis

## 2026-05-29 08:55:18.490146 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified

## 2026-05-29 08:55:18.718012 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar

## 2026-05-29 08:55:18.944231 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica

## 2026-05-29 08:55:19.168151 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8

## 2026-05-29 08:55:19.395837 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile

## 2026-05-29 08:55:19.61727 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47

## 2026-05-29 08:55:19.836578 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA

## 2026-05-29 08:55:20.061155 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila

## 2026-05-29 08:55:20.290105 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae

## 2026-05-29 08:55:20.514107 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus

## 2026-05-29 08:55:22.896735 INFO::Plotting data for metadata number 5, age
## 2026-05-29 08:55:22.898147 INFO::Creating scatter plot for continuous data, age vs Haemophilus.parainfluenzae

## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## ℹ The deprecated feature was likely used in the Maaslin2 package.
##   Please report the issue at <https://github.com/biobakery/maaslin2/issues>.
## This warning is displayed once per session.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:23.180434 INFO::Creating scatter plot for continuous data, age vs Bifidobacterium.pseudocatenulatum

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:23.467124 INFO::Creating scatter plot for continuous data, age vs Faecalibacterium.prausnitzii

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:23.697526 INFO::Creating scatter plot for continuous data, age vs Clostridium.clostridioforme

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:23.93828 INFO::Creating scatter plot for continuous data, age vs Veillonella.parvula

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:24.160686 INFO::Creating scatter plot for continuous data, age vs Subdoligranulum.unclassified

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:24.384 INFO::Creating scatter plot for continuous data, age vs Clostridium.symbiosum

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:24.622172 INFO::Creating scatter plot for continuous data, age vs Ruminococcus.gnavus

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:24.861792 INFO::Creating scatter plot for continuous data, age vs Dialister.invisus

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:25.090075 INFO::Creating scatter plot for continuous data, age vs Veillonella.dispar

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:25.314398 INFO::Creating scatter plot for continuous data, age vs Veillonella.unclassified

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:25.604202 INFO::Creating scatter plot for continuous data, age vs Bacteroides.thetaiotaomicron

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:25.837087 INFO::Creating scatter plot for continuous data, age vs Ruminococcus.bromii

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:26.070397 INFO::Creating scatter plot for continuous data, age vs Bacteroides.intestinalis

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:26.29524 INFO::Creating scatter plot for continuous data, age vs Eubacterium.siraeum

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:26.530529 INFO::Creating scatter plot for continuous data, age vs Prevotella.copri

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:26.762506 INFO::Creating scatter plot for continuous data, age vs Alistipes.unclassified

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:26.985822 INFO::Creating scatter plot for continuous data, age vs Bacteroidales.bacterium.ph8

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:27.224351 INFO::Creating scatter plot for continuous data, age vs Bifidobacterium.longum

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:27.44905 INFO::Creating scatter plot for continuous data, age vs Akkermansia.muciniphila

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:27.700041 INFO::Creating scatter plot for continuous data, age vs Collinsella.aerofaciens

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:27.927801 INFO::Creating scatter plot for continuous data, age vs Parabacteroides.distasonis

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).

## 2026-05-29 08:55:30.439436 INFO::Plotting data for metadata number 6, diagnosis
## 2026-05-29 08:55:30.441049 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis

## 2026-05-29 08:55:30.692871 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila

## 2026-05-29 08:55:30.959286 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae

## 2026-05-29 08:55:31.236718 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis

## 2026-05-29 08:55:31.511316 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified

## 2026-05-29 08:55:31.777362 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme

## 2026-05-29 08:55:32.057318 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii

## 2026-05-29 08:55:32.318199 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii

## 2026-05-29 08:55:32.604723 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum

## 2026-05-29 08:55:32.869605 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum

## 2026-05-29 08:55:33.143987 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans

## 2026-05-29 08:55:33.459817 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii

## 2026-05-29 08:55:33.73527 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii

## 2026-05-29 08:55:34.021833 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii

## 2026-05-29 08:55:34.292096 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii

## 2026-05-29 08:55:34.579231 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified

## 2026-05-29 08:55:34.847013 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum

## 2026-05-29 08:55:35.130661 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis

## 2026-05-29 08:55:35.419886 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified

## 2026-05-29 08:55:35.703188 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii

## 2026-05-29 08:55:35.968712 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum

## 2026-05-29 08:55:36.257658 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis

## 2026-05-29 08:55:36.540786 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis

## 2026-05-29 08:55:36.827878 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila

## 2026-05-29 08:55:37.146638 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis

## 2026-05-29 08:55:37.429727 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified

## 2026-05-29 08:55:37.733315 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum

## 2026-05-29 08:55:38.028084 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii

## 2026-05-29 08:55:38.330787 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified

## 2026-05-29 08:55:38.625814 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris

## 2026-05-29 08:55:38.908043 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus

## 2026-05-29 08:55:39.212532 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus

## 2026-05-29 08:55:39.522421 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis

## 2026-05-29 08:55:39.842505 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale

## 2026-05-29 08:55:40.151881 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus

## 2026-05-29 08:55:40.46735 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis

## 2026-05-29 08:55:41.091446 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale

## 2026-05-29 08:55:41.33318 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii

## 2026-05-29 08:55:41.575917 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus

## 2026-05-29 08:55:41.812365 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii

## 2026-05-29 08:55:42.048505 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis

## 2026-05-29 08:55:42.28842 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae

## 2026-05-29 08:55:42.528623 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.siraeum

Session Info

Session info from running the demo in R can be displayed with the following command.

sessionInfo()

## R version 4.6.0 (2026-04-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.4 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] Maaslin2_1.26.0
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.6        biglm_0.9-3         xfun_0.57          
##  [4] bslib_0.11.0        ggplot2_4.0.3       lattice_0.22-9     
##  [7] numDeriv_2016.8-1.1 vctrs_0.7.3         tools_4.6.0        
## [10] Rdpack_2.6.6        generics_0.1.4      parallel_4.6.0     
## [13] tibble_3.3.1        DEoptimR_1.1-4      cluster_2.1.8.2    
## [16] pkgconfig_2.0.3     logging_0.10-111    pheatmap_1.0.13    
## [19] Matrix_1.7-5        data.table_1.18.4   RColorBrewer_1.1-3 
## [22] S7_0.2.2            lifecycle_1.0.5     compiler_4.6.0     
## [25] farver_2.1.2        lmerTest_3.2-1      permute_0.9-10     
## [28] htmltools_0.5.9     sys_3.4.3           buildtools_1.0.0   
## [31] sass_0.4.10         hash_2.2.6.4        yaml_2.3.12        
## [34] pillar_1.11.1       nloptr_2.2.1        crayon_1.5.3       
## [37] jquerylib_0.1.4     MASS_7.3-65         cachem_1.1.0       
## [40] vegan_2.7-5         reformulas_0.4.4    boot_1.3-32        
## [43] nlme_3.1-169        robustbase_0.99-7   tidyselect_1.2.1   
## [46] digest_0.6.39       mvtnorm_1.3-7       dplyr_1.2.1        
## [49] labeling_0.4.3      maketools_1.3.2     splines_4.6.0      
## [52] pcaPP_2.0-5         fastmap_1.2.0       grid_4.6.0         
## [55] cli_3.6.6           magrittr_2.0.5      withr_3.0.2        
## [58] scales_1.4.0        rmarkdown_2.31      lme4_2.0-1         
## [61] pbapply_1.7-4       evaluate_1.0.5      knitr_1.51         
## [64] rbibutils_2.4.1     mgcv_1.9-4          rlang_1.2.0        
## [67] Rcpp_1.1.1-1.1      glue_1.8.1          optparse_1.8.2     
## [70] DBI_1.3.0           minqa_1.2.8         jsonlite_2.0.0     
## [73] R6_2.6.1

Options

Run MaAsLin2 help to print a list of the options and the default settings.

$ Maaslin2.R –help Usage: ./R/Maaslin2.R options <data.tsv> <metadata.tsv>

Options: -h, –help Show this help message and exit

-a MIN_ABUNDANCE, --min_abundance=MIN_ABUNDANCE
    The minimum abundance for each feature [ Default: 0 ]

-p MIN_PREVALENCE, --min_prevalence=MIN_PREVALENCE
    The minimum percent of samples for which a feature 
    is detected at minimum abundance [ Default: 0.1 ]

-b MIN_VARIANCE, --min_variance=MIN_VARIANCE
    Keep features with variance greater than [ Default: 0.0 ]

-s MAX_SIGNIFICANCE, --max_significance=MAX_SIGNIFICANCE
    The q-value threshold for significance [ Default: 0.25 ]

-n NORMALIZATION, --normalization=NORMALIZATION
    The normalization method to apply [ Default: TSS ]
    [ Choices: TSS, CLR, CSS, NONE, TMM ]

-t TRANSFORM, --transform=TRANSFORM
    The transform to apply [ Default: LOG ]
    [ Choices: LOG, LOGIT, AST, NONE ]

-m ANALYSIS_METHOD, --analysis_method=ANALYSIS_METHOD
    The analysis method to apply [ Default: LM ]
    [ Choices: LM, CPLM, NEGBIN, ZINB ]

-r RANDOM_EFFECTS, --random_effects=RANDOM_EFFECTS
    The random effects for the model, comma-delimited
    for multiple effects [ Default: none ]

-f FIXED_EFFECTS, --fixed_effects=FIXED_EFFECTS
    The fixed effects for the model, comma-delimited
    for multiple effects [ Default: all ]

-c CORRECTION, --correction=CORRECTION
    The correction method for computing the 
    q-value [ Default: BH ]

-z STANDARDIZE, --standardize=STANDARDIZE
    Apply z-score so continuous metadata are 
    on the same scale [ Default: TRUE ]

-l PLOT_HEATMAP, --plot_heatmap=PLOT_HEATMAP
    Generate a heatmap for the significant 
    associations [ Default: TRUE ]

-i HEATMAP_FIRST_N, --heatmap_first_n=HEATMAP_FIRST_N
    In heatmap, plot top N features with significant 
    associations [ Default: TRUE ]

-o PLOT_SCATTER, --plot_scatter=PLOT_SCATTER
    Generate scatter plots for the significant
    associations [ Default: TRUE ]
    
-g MAX_PNGS, --max_pngs=MAX_PNGS
    The maximum number of scatter plots for signficant associations 
    to save as png files [ Default: 10 ]

-O SAVE_SCATTER, --save_scatter=SAVE_SCATTER
    Save all scatter plot ggplot objects
    to an RData file [ Default: FALSE ]

-e CORES, --cores=CORES
    The number of R processes to run in parallel
    [ Default: 1 ]
    
-j SAVE_MODELS --save_models=SAVE_MODELS
    Return the full model outputs and save to an RData file
    [ Default: FALSE ]

-d REFERENCE, --reference=REFERENCE
    The factor to use as a reference level for a categorical variable 
    provided as a string of 'variable,reference', semi-colon delimited for 
    multiple variables. Not required if metadata is passed as a factor or 
    for variables with less than two levels but can be set regardless.
    [ Default: NA ]

Troubleshooting

Question: When I run from the command line I see the error Maaslin2.R: command not found. How do I fix this?
- Answer: Provide the full path to the executable when running Maaslin2.R.
Question: When I run as a function I see the error Error in library(Maaslin2): there is no package called 'Maaslin2'. How do I fix this?
- Answer: Install the R package and then try loading the library again.
Question: When I try to install the R package I see errors about dependencies not being installed. Why is this?
- Answer: Installing the R package will not automatically install the packages MaAsLin2 requires. Please install the dependencies and then install the MaAsLin2 R package.

- MaAsLin2 User Manual

Maaslin2