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"
## 2026-07-04 15:52:05.966251 INFO::Writing function arguments to log file
## 2026-07-04 15:52:06.042254 INFO::Verifying options selected are valid
## 2026-07-04 15:52:06.063034 INFO::Determining format of input files
## 2026-07-04 15:52:06.063791 INFO::Input format is data samples as rows and metadata samples as rows
## 2026-07-04 15:52:06.067066 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2026-07-04 15:52:06.067854 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2026-07-04 15:52:06.069467 INFO::Filter data based on min abundance and min prevalence
## 2026-07-04 15:52:06.069983 INFO::Total samples in data: 1595
## 2026-07-04 15:52:06.070594 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2026-07-04 15:52:06.07418 INFO::Total filtered features: 0
## 2026-07-04 15:52:06.074813 INFO::Filtered feature names from abundance and prevalence filtering:
## 2026-07-04 15:52:06.081201 INFO::Total filtered features with variance filtering: 0
## 2026-07-04 15:52:06.081792 INFO::Filtered feature names from variance filtering:
## 2026-07-04 15:52:06.082278 INFO::Running selected normalization method: TSS
## 2026-07-04 15:52:06.820589 INFO::Bypass z-score application to metadata
## 2026-07-04 15:52:06.821337 INFO::Running selected transform method: LOG
## 2026-07-04 15:52:06.841546 INFO::Running selected analysis method: LM
## 2026-07-04 15:52:07.061982 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis

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

## 2026-07-04 15:52:07.44119 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2026-07-04 15:52:07.538446 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2026-07-04 15:52:07.682151 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum

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

## 2026-07-04 15:52:07.76825 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2026-07-04 15:52:07.870951 INFO::Fitting model to feature number 6, Bacteroides.caccae

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

## 2026-07-04 15:52:07.957945 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2026-07-04 15:52:08.050839 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2026-07-04 15:52:08.145081 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2026-07-04 15:52:08.240023 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2026-07-04 15:52:08.332431 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

## 2026-07-04 15:52:08.409663 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

## 2026-07-04 15:52:08.501456 INFO::Fitting model to feature number 12, Bacteroides.fragilis

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

## 2026-07-04 15:52:08.587592 INFO::Fitting model to feature number 13, Bacteroides.intestinalis

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

## 2026-07-04 15:52:08.680932 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2026-07-04 15:52:08.769 INFO::Fitting model to feature number 15, Bacteroides.ovatus

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

## 2026-07-04 15:52:08.856178 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2026-07-04 15:52:09.11924 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2026-07-04 15:52:09.208598 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron

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

## 2026-07-04 15:52:09.294853 INFO::Fitting model to feature number 19, Bacteroides.uniformis

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

## 2026-07-04 15:52:09.399196 INFO::Fitting model to feature number 20, Bacteroides.vulgatus

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

## 2026-07-04 15:52:09.4872 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens

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

## 2026-07-04 15:52:09.575531 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2026-07-04 15:52:09.667208 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2026-07-04 15:52:09.766979 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2026-07-04 15:52:09.860639 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2026-07-04 15:52:09.951942 INFO::Fitting model to feature number 26, Parabacteroides.distasonis

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

## 2026-07-04 15:52:10.046347 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2026-07-04 15:52:10.13942 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2026-07-04 15:52:10.231544 INFO::Fitting model to feature number 29, Parabacteroides.unclassified

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

## 2026-07-04 15:52:10.323289 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2026-07-04 15:52:10.415675 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2026-07-04 15:52:10.505871 INFO::Fitting model to feature number 32, Prevotella.copri

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

## 2026-07-04 15:52:10.598508 INFO::Fitting model to feature number 33, Alistipes.finegoldii

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

## 2026-07-04 15:52:10.683341 INFO::Fitting model to feature number 34, Alistipes.onderdonkii

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

## 2026-07-04 15:52:10.772609 INFO::Fitting model to feature number 35, Alistipes.putredinis

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

## 2026-07-04 15:52:10.865123 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2026-07-04 15:52:10.956543 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2026-07-04 15:52:11.043802 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2026-07-04 15:52:11.145013 INFO::Fitting model to feature number 39, Clostridium.bolteae

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

## 2026-07-04 15:52:11.235806 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

## 2026-07-04 15:52:11.48886 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

## 2026-07-04 15:52:11.577065 INFO::Fitting model to feature number 41, Clostridium.clostridioforme

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

## 2026-07-04 15:52:11.663048 INFO::Fitting model to feature number 42, Clostridium.hathewayi

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

## 2026-07-04 15:52:11.74951 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2026-07-04 15:52:11.85862 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2026-07-04 15:52:11.961306 INFO::Fitting model to feature number 45, Clostridium.symbiosum

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

## 2026-07-04 15:52:12.048043 INFO::Fitting model to feature number 46, Flavonifractor.plautii

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

## 2026-07-04 15:52:12.137378 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2026-07-04 15:52:12.226218 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2026-07-04 15:52:12.320081 INFO::Fitting model to feature number 49, Eubacterium.rectale

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

## 2026-07-04 15:52:12.416957 INFO::Fitting model to feature number 50, Eubacterium.siraeum

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

## 2026-07-04 15:52:12.502908 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31

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

## 2026-07-04 15:52:12.590918 INFO::Fitting model to feature number 52, Eubacterium.ventriosum

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

## 2026-07-04 15:52:12.67434 INFO::Fitting model to feature number 53, Ruminococcus.gnavus

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

## 2026-07-04 15:52:12.767725 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2026-07-04 15:52:12.856 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2026-07-04 15:52:12.945793 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2026-07-04 15:52:13.03837 INFO::Fitting model to feature number 57, Dorea.longicatena

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

## 2026-07-04 15:52:13.129403 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA

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

## 2026-07-04 15:52:13.229923 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA

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

## 2026-07-04 15:52:13.319273 INFO::Fitting model to feature number 60, Roseburia.hominis

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

## 2026-07-04 15:52:13.410447 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2026-07-04 15:52:13.499063 INFO::Fitting model to feature number 62, Roseburia.inulinivorans

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

## 2026-07-04 15:52:13.593174 INFO::Fitting model to feature number 63, Roseburia.unclassified

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

## 2026-07-04 15:52:13.682198 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2026-07-04 15:52:13.778426 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2026-07-04 15:52:13.867765 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2026-07-04 15:52:13.966342 INFO::Fitting model to feature number 67, Ruminococcus.bromii

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

## 2026-07-04 15:52:14.049066 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2026-07-04 15:52:14.1363 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2026-07-04 15:52:14.228439 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified

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

## 2026-07-04 15:52:14.332048 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2026-07-04 15:52:14.41833 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2026-07-04 15:52:14.510938 INFO::Fitting model to feature number 73, Dialister.invisus

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

## 2026-07-04 15:52:14.597649 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2026-07-04 15:52:14.690211 INFO::Fitting model to feature number 75, Veillonella.dispar

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

## 2026-07-04 15:52:14.78443 INFO::Fitting model to feature number 76, Veillonella.parvula

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

## 2026-07-04 15:52:14.868617 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2026-07-04 15:52:14.956732 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2026-07-04 15:52:15.048554 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2026-07-04 15:52:15.143512 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2026-07-04 15:52:15.235755 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2026-07-04 15:52:15.332145 INFO::Fitting model to feature number 82, Escherichia.coli
## 2026-07-04 15:52:15.424351 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2026-07-04 15:52:15.509829 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae

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

## 2026-07-04 15:52:15.60078 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae

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

## 2026-07-04 15:52:15.688872 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2026-07-04 15:52:15.780924 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2026-07-04 15:52:15.903152 INFO::Counting total values for each feature
## 2026-07-04 15:52:15.922945 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2026-07-04 15:52:15.984215 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2026-07-04 15:52:16.045129 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2026-07-04 15:52:16.132065 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2026-07-04 15:52:16.170065 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2026-07-04 15:52:16.19192 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2026-07-04 15:52:16.195352 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2026-07-04 15:52:16.198532 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
## 2026-07-04 15:52:16.200042 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2026-07-04 15:52:16.603306 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2026-07-04 15:52:16.607157 INFO::Plotting associations from most to least significant, grouped by metadata
## 2026-07-04 15:52:16.607759 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2026-07-04 15:52:16.608792 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii

## 2026-07-04 15:52:16.912313 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified

## 2026-07-04 15:52:17.166489 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis

## 2026-07-04 15:52:17.410149 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale

## 2026-07-04 15:52:17.654823 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus

## 2026-07-04 15:52:17.898667 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus

## 2026-07-04 15:52:18.140798 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum

## 2026-07-04 15:52:18.382109 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified

## 2026-07-04 15:52:18.623577 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans

## 2026-07-04 15:52:18.873107 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis

## 2026-07-04 15:52:19.121664 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron

## 2026-07-04 15:52:19.366015 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis

## 2026-07-04 15:52:19.610884 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis

## 2026-07-04 15:52:19.853445 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei

## 2026-07-04 15:52:20.09892 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii

## 2026-07-04 15:52:20.342113 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens

## 2026-07-04 15:52:20.818745 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum

## 2026-07-04 15:52:21.060504 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena

## 2026-07-04 15:52:21.303242 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae

## 2026-07-04 15:52:21.546163 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-07-04 15:52:21.782827 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli

## 2026-07-04 15:52:22.022271 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae

## 2026-07-04 15:52:22.258973 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified

## 2026-07-04 15:52:22.48759 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii

## 2026-07-04 15:52:22.727225 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens

## 2026-07-04 15:52:22.962595 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris

## 2026-07-04 15:52:23.200289 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes

## 2026-07-04 15:52:23.4387 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis

## 2026-07-04 15:52:23.681877 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii

## 2026-07-04 15:52:23.922644 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii

## 2026-07-04 15:52:24.155655 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis

## 2026-07-04 15:52:24.399896 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara

## 2026-07-04 15:52:24.636675 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum

## 2026-07-04 15:52:24.90505 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae

## 2026-07-04 15:52:25.150216 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified

## 2026-07-04 15:52:25.401889 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens

## 2026-07-04 15:52:25.64809 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus

## 2026-07-04 15:52:25.899075 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme

## 2026-07-04 15:52:26.147319 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii

## 2026-07-04 15:52:26.40381 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii

## 2026-07-04 15:52:26.652637 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum

## 2026-07-04 15:52:26.901977 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris

## 2026-07-04 15:52:27.158509 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47

## 2026-07-04 15:52:27.399858 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus

## 2026-07-04 15:52:27.644247 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii

## 2026-07-04 15:52:27.888805 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis

## 2026-07-04 15:52:28.144513 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified

## 2026-07-04 15:52:28.394847 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques

## 2026-07-04 15:52:28.635963 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified

## 2026-07-04 15:52:28.899325 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus

## 2026-07-04 15:52:29.174951 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis

## 2026-07-04 15:52:29.431438 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified

## 2026-07-04 15:52:29.689807 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified

## 2026-07-04 15:52:29.945806 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis

## 2026-07-04 15:52:30.202879 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis

## 2026-07-04 15:52:30.465136 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31

## 2026-07-04 15:52:30.717822 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae

## 2026-07-04 15:52:30.968214 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8

## 2026-07-04 15:52:31.219694 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae

## 2026-07-04 15:52:31.477957 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii

## 2026-07-04 15:52:31.744925 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii

## 2026-07-04 15:52:32.004092 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum

## 2026-07-04 15:52:32.254487 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA

## 2026-07-04 15:52:34.90148 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2026-07-04 15:52:34.902752 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified

## 2026-07-04 15:52:35.142776 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii

## 2026-07-04 15:52:35.421216 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae

## 2026-07-04 15:52:35.689873 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified

## 2026-07-04 15:52:35.949117 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis

## 2026-07-04 15:52:36.213712 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum

## 2026-07-04 15:52:36.480252 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus

## 2026-07-04 15:52:36.747407 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis

## 2026-07-04 15:52:37.022667 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii

## 2026-07-04 15:52:37.29476 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale

## 2026-07-04 15:52:37.560661 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis

## 2026-07-04 15:52:37.842264 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis

## 2026-07-04 15:52:38.112437 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-07-04 15:52:38.38022 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii

## 2026-07-04 15:52:38.697148 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens

## 2026-07-04 15:52:38.971032 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris

## 2026-07-04 15:52:39.240737 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii

## 2026-07-04 15:52:39.50858 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis

## 2026-07-04 15:52:39.7936 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum

## 2026-07-04 15:52:40.055411 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus

## 2026-07-04 15:52:40.320216 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii

## 2026-07-04 15:52:40.606916 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii

## 2026-07-04 15:52:40.871845 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae

## 2026-07-04 15:52:41.146756 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus

## 2026-07-04 15:52:41.42781 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum

## 2026-07-04 15:52:41.694684 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae

## 2026-07-04 15:52:41.973649 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae

## 2026-07-04 15:52:42.234273 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum

## 2026-07-04 15:52:42.504521 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis

## 2026-07-04 15:52:42.810337 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii

## 2026-07-04 15:52:43.086242 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques

## 2026-07-04 15:52:43.346726 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8

## 2026-07-04 15:52:43.620441 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum

## 2026-07-04 15:52:43.901617 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum

## 2026-07-04 15:52:44.175159 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis

## 2026-07-04 15:52:44.438494 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens

## 2026-07-04 15:52:44.723561 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi

## 2026-07-04 15:52:44.994236 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified

## 2026-07-04 15:52:45.278664 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens

## 2026-07-04 15:52:45.561483 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus

## 2026-07-04 15:52:45.84314 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae

## 2026-07-04 15:52:46.126605 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus

## 2026-07-04 15:52:46.41494 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris

## 2026-07-04 15:52:46.700573 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47

## 2026-07-04 15:52:49.397486 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2026-07-04 15:52:49.39872 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii

## 2026-07-04 15:52:49.617143 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale

## 2026-07-04 15:52:49.856992 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31

## 2026-07-04 15:52:50.098611 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis

## 2026-07-04 15:52:50.331028 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified

## 2026-07-04 15:52:50.570496 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-07-04 15:52:50.81287 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques

## 2026-07-04 15:52:51.057202 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum

## 2026-07-04 15:52:51.300896 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus

## 2026-07-04 15:52:51.544216 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli

## 2026-07-04 15:52:51.785748 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum

## 2026-07-04 15:52:52.060589 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified

## 2026-07-04 15:52:52.314413 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis

## 2026-07-04 15:52:52.563808 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens

## 2026-07-04 15:52:52.816929 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae

## 2026-07-04 15:52:53.078519 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii

## 2026-07-04 15:52:53.32219 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus

## 2026-07-04 15:52:53.566884 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified

## 2026-07-04 15:52:53.827059 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis

## 2026-07-04 15:52:54.07013 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii

## 2026-07-04 15:52:54.315056 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans

## 2026-07-04 15:52:54.569942 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii

## 2026-07-04 15:52:54.818041 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified

## 2026-07-04 15:52:55.071767 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii

## 2026-07-04 15:52:55.313553 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis

## 2026-07-04 15:52:55.567797 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri

## 2026-07-04 15:52:55.814806 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei

## 2026-07-04 15:52:56.097366 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis

## 2026-07-04 15:52:56.357885 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii

## 2026-07-04 15:52:58.988028 INFO::Plotting data for metadata number 4, antibiotics
## 2026-07-04 15:52:58.989472 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans

## 2026-07-04 15:52:59.225164 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis

## 2026-07-04 15:52:59.487576 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale

## 2026-07-04 15:52:59.740675 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus

## 2026-07-04 15:52:59.99931 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis

## 2026-07-04 15:53:00.255284 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena

## 2026-07-04 15:53:00.503545 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus

## 2026-07-04 15:53:00.794909 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii

## 2026-07-04 15:53:01.048676 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum

## 2026-07-04 15:53:01.29874 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae

## 2026-07-04 15:53:01.55772 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis

## 2026-07-04 15:53:01.827115 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii

## 2026-07-04 15:53:02.083458 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii

## 2026-07-04 15:53:02.35094 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified

## 2026-07-04 15:53:02.612153 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum

## 2026-07-04 15:53:02.864086 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-07-04 15:53:03.130831 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii

## 2026-07-04 15:53:03.383519 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31

## 2026-07-04 15:53:03.643469 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis

## 2026-07-04 15:53:03.891948 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii

## 2026-07-04 15:53:04.150805 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis

## 2026-07-04 15:53:04.444362 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens

## 2026-07-04 15:53:04.703433 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens

## 2026-07-04 15:53:04.965174 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron

## 2026-07-04 15:53:05.247231 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii

## 2026-07-04 15:53:05.509726 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae

## 2026-07-04 15:53:05.775534 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum

## 2026-07-04 15:53:06.042313 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques

## 2026-07-04 15:53:06.308035 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum

## 2026-07-04 15:53:06.580125 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis

## 2026-07-04 15:53:06.851151 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified

## 2026-07-04 15:53:07.109802 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar

## 2026-07-04 15:53:07.383475 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica

## 2026-07-04 15:53:07.649131 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8

## 2026-07-04 15:53:07.912755 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile

## 2026-07-04 15:53:08.218844 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47

## 2026-07-04 15:53:08.481118 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA

## 2026-07-04 15:53:08.763807 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila

## 2026-07-04 15:53:09.037685 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae

## 2026-07-04 15:53:09.312108 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus

## 2026-07-04 15:53:12.011084 INFO::Plotting data for metadata number 5, age
## 2026-07-04 15:53:12.012779 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()`).

## 2026-07-04 15:53:12.333214 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()`).

## 2026-07-04 15:53:12.895313 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()`).

## 2026-07-04 15:53:13.107076 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()`).

## 2026-07-04 15:53:13.333082 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()`).

## 2026-07-04 15:53:13.545063 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()`).

## 2026-07-04 15:53:13.760299 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()`).

## 2026-07-04 15:53:13.983881 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()`).

## 2026-07-04 15:53:14.204619 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()`).

## 2026-07-04 15:53:14.422725 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()`).

## 2026-07-04 15:53:14.64433 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()`).

## 2026-07-04 15:53:14.855617 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()`).

## 2026-07-04 15:53:15.070165 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()`).

## 2026-07-04 15:53:15.288718 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()`).

## 2026-07-04 15:53:15.502078 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()`).

## 2026-07-04 15:53:15.717116 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()`).

## 2026-07-04 15:53:15.931062 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()`).

## 2026-07-04 15:53:16.141607 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()`).

## 2026-07-04 15:53:16.352563 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()`).

## 2026-07-04 15:53:16.572005 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()`).

## 2026-07-04 15:53:16.828172 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()`).

## 2026-07-04 15:53:17.054163 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()`).

## 2026-07-04 15:53:19.448806 INFO::Plotting data for metadata number 6, diagnosis
## 2026-07-04 15:53:19.450208 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis

## 2026-07-04 15:53:19.682447 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila

## 2026-07-04 15:53:19.94521 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae

## 2026-07-04 15:53:20.198578 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis

## 2026-07-04 15:53:20.458352 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified

## 2026-07-04 15:53:20.724065 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme

## 2026-07-04 15:53:20.977206 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii

## 2026-07-04 15:53:21.227729 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii

## 2026-07-04 15:53:21.517619 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum

## 2026-07-04 15:53:21.776942 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum

## 2026-07-04 15:53:22.038585 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans

## 2026-07-04 15:53:22.301057 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii

## 2026-07-04 15:53:22.580785 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii

## 2026-07-04 15:53:22.838791 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii

## 2026-07-04 15:53:23.093974 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii

## 2026-07-04 15:53:23.361265 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified

## 2026-07-04 15:53:23.609329 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum

## 2026-07-04 15:53:23.875215 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis

## 2026-07-04 15:53:24.13375 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified

## 2026-07-04 15:53:24.399553 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii

## 2026-07-04 15:53:24.660147 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum

## 2026-07-04 15:53:24.930901 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis

## 2026-07-04 15:53:25.182794 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis

## 2026-07-04 15:53:25.485726 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila

## 2026-07-04 15:53:25.745413 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis

## 2026-07-04 15:53:26.007519 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified

## 2026-07-04 15:53:26.282024 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum

## 2026-07-04 15:53:26.566832 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii

## 2026-07-04 15:53:26.829311 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified

## 2026-07-04 15:53:27.105977 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris

## 2026-07-04 15:53:27.369141 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus

## 2026-07-04 15:53:27.645498 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus

## 2026-07-04 15:53:27.90461 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis

## 2026-07-04 15:53:28.182823 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale

## 2026-07-04 15:53:28.446505 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus

## 2026-07-04 15:53:28.724785 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis

## 2026-07-04 15:53:28.993874 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale

## 2026-07-04 15:53:29.259433 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii

## 2026-07-04 15:53:29.568627 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus

## 2026-07-04 15:53:29.843944 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii

## 2026-07-04 15:53:30.115129 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis

## 2026-07-04 15:53:30.399651 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae

## 2026-07-04 15:53:30.680764 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 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04 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-r0.3.32.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_0.59          
##  [4] bslib_0.11.0        ggplot2_4.0.3       lattice_0.22-9     
##  [7] numDeriv_2016.8-1.1 vctrs_0.7.3         tools_4.6.1        
## [10] Rdpack_2.6.6        generics_0.1.4      parallel_4.6.1     
## [13] tibble_3.3.1        DEoptimR_1.2-0      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_4.6.1     
## [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_1.4-1       dplyr_1.2.1        
## [49] labeling_0.4.3      maketools_1.3.2     splines_4.6.1      
## [52] pcaPP_2.0-5         fastmap_1.2.0       grid_4.6.1         
## [55] cli_3.6.6           magrittr_2.0.5      withr_3.0.3        
## [58] scales_1.4.0        rmarkdown_2.31      otel_0.2.0         
## [61] lme4_2.0-1          pbapply_1.7-4       evaluate_1.0.5     
## [64] knitr_1.51          rbibutils_2.4.1     mgcv_1.9-4         
## [67] rlang_1.2.0         Rcpp_1.1.1-1.1      glue_1.8.1         
## [70] optparse_1.8.2      DBI_1.3.0           minqa_1.2.8        
## [73] jsonlite_2.0.0      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