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"
## 2026-04-29 16:25:53.17892 INFO::Writing function arguments to log file
## 2026-04-29 16:25:53.251963 INFO::Verifying options selected are valid
## 2026-04-29 16:25:53.27217 INFO::Determining format of input files
## 2026-04-29 16:25:53.272909 INFO::Input format is data samples as rows and metadata samples as rows
## 2026-04-29 16:25:53.276594 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2026-04-29 16:25:53.277425 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2026-04-29 16:25:53.279041 INFO::Filter data based on min abundance and min prevalence
## 2026-04-29 16:25:53.279591 INFO::Total samples in data: 1595
## 2026-04-29 16:25:53.280082 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2026-04-29 16:25:53.284046 INFO::Total filtered features: 0
## 2026-04-29 16:25:53.284769 INFO::Filtered feature names from abundance and prevalence filtering:
## 2026-04-29 16:25:53.291642 INFO::Total filtered features with variance filtering: 0
## 2026-04-29 16:25:53.292297 INFO::Filtered feature names from variance filtering:
## 2026-04-29 16:25:53.292904 INFO::Running selected normalization method: TSS
## 2026-04-29 16:25:54.02369 INFO::Bypass z-score application to metadata
## 2026-04-29 16:25:54.024444 INFO::Running selected transform method: LOG
## 2026-04-29 16:25:54.045007 INFO::Running selected analysis method: LM
## 2026-04-29 16:25:54.262297 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis

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

## 2026-04-29 16:25:54.826937 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2026-04-29 16:25:54.922668 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2026-04-29 16:25:55.011306 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum

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

## 2026-04-29 16:25:55.101895 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2026-04-29 16:25:55.198758 INFO::Fitting model to feature number 6, Bacteroides.caccae

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

## 2026-04-29 16:25:55.296718 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2026-04-29 16:25:55.384287 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2026-04-29 16:25:55.478788 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2026-04-29 16:25:55.573774 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2026-04-29 16:25:55.665453 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

## 2026-04-29 16:25:55.73774 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

## 2026-04-29 16:25:55.829898 INFO::Fitting model to feature number 12, Bacteroides.fragilis

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

## 2026-04-29 16:25:55.916016 INFO::Fitting model to feature number 13, Bacteroides.intestinalis

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

## 2026-04-29 16:25:56.010465 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2026-04-29 16:25:56.09915 INFO::Fitting model to feature number 15, Bacteroides.ovatus

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

## 2026-04-29 16:25:56.182833 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2026-04-29 16:25:56.27779 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2026-04-29 16:25:56.367191 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron

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

## 2026-04-29 16:25:56.456727 INFO::Fitting model to feature number 19, Bacteroides.uniformis

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

## 2026-04-29 16:25:56.542991 INFO::Fitting model to feature number 20, Bacteroides.vulgatus

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

## 2026-04-29 16:25:56.628948 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens

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

## 2026-04-29 16:25:56.720105 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2026-04-29 16:25:56.806783 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2026-04-29 16:25:56.902521 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2026-04-29 16:25:56.999542 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2026-04-29 16:25:57.087785 INFO::Fitting model to feature number 26, Parabacteroides.distasonis

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

## 2026-04-29 16:25:57.180024 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2026-04-29 16:25:57.270507 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2026-04-29 16:25:57.360979 INFO::Fitting model to feature number 29, Parabacteroides.unclassified

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

## 2026-04-29 16:25:57.451326 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2026-04-29 16:25:57.541599 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2026-04-29 16:25:57.636321 INFO::Fitting model to feature number 32, Prevotella.copri

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

## 2026-04-29 16:25:57.722252 INFO::Fitting model to feature number 33, Alistipes.finegoldii

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

## 2026-04-29 16:25:57.806927 INFO::Fitting model to feature number 34, Alistipes.onderdonkii

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

## 2026-04-29 16:25:57.902143 INFO::Fitting model to feature number 35, Alistipes.putredinis

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

## 2026-04-29 16:25:57.988806 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2026-04-29 16:25:58.085817 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2026-04-29 16:25:58.171654 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2026-04-29 16:25:58.262807 INFO::Fitting model to feature number 39, Clostridium.bolteae

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

## 2026-04-29 16:25:58.358306 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

## 2026-04-29 16:25:58.430531 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

## 2026-04-29 16:25:58.51743 INFO::Fitting model to feature number 41, Clostridium.clostridioforme

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

## 2026-04-29 16:25:58.607179 INFO::Fitting model to feature number 42, Clostridium.hathewayi

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

## 2026-04-29 16:25:58.693159 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2026-04-29 16:25:58.795568 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2026-04-29 16:25:58.882559 INFO::Fitting model to feature number 45, Clostridium.symbiosum

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

## 2026-04-29 16:25:58.971934 INFO::Fitting model to feature number 46, Flavonifractor.plautii

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

## 2026-04-29 16:25:59.065948 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2026-04-29 16:25:59.15351 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2026-04-29 16:25:59.250902 INFO::Fitting model to feature number 49, Eubacterium.rectale

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

## 2026-04-29 16:25:59.342532 INFO::Fitting model to feature number 50, Eubacterium.siraeum

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

## 2026-04-29 16:25:59.42685 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31

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

## 2026-04-29 16:25:59.519599 INFO::Fitting model to feature number 52, Eubacterium.ventriosum

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

## 2026-04-29 16:25:59.60072 INFO::Fitting model to feature number 53, Ruminococcus.gnavus

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

## 2026-04-29 16:25:59.692514 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2026-04-29 16:25:59.780531 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2026-04-29 16:25:59.867443 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2026-04-29 16:25:59.965173 INFO::Fitting model to feature number 57, Dorea.longicatena

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

## 2026-04-29 16:26:00.053685 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA

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

## 2026-04-29 16:26:00.14472 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA

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

## 2026-04-29 16:26:00.238802 INFO::Fitting model to feature number 60, Roseburia.hominis

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

## 2026-04-29 16:26:00.327363 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2026-04-29 16:26:00.59167 INFO::Fitting model to feature number 62, Roseburia.inulinivorans

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

## 2026-04-29 16:26:00.678617 INFO::Fitting model to feature number 63, Roseburia.unclassified

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

## 2026-04-29 16:26:00.771485 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2026-04-29 16:26:00.885513 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2026-04-29 16:26:00.992559 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2026-04-29 16:26:01.090152 INFO::Fitting model to feature number 67, Ruminococcus.bromii

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

## 2026-04-29 16:26:01.172893 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2026-04-29 16:26:01.26053 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2026-04-29 16:26:01.35242 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified

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

## 2026-04-29 16:26:01.445025 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2026-04-29 16:26:01.530533 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2026-04-29 16:26:01.621048 INFO::Fitting model to feature number 73, Dialister.invisus

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

## 2026-04-29 16:26:01.708146 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2026-04-29 16:26:01.803625 INFO::Fitting model to feature number 75, Veillonella.dispar

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

## 2026-04-29 16:26:01.908939 INFO::Fitting model to feature number 76, Veillonella.parvula

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

## 2026-04-29 16:26:02.002997 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2026-04-29 16:26:02.092971 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2026-04-29 16:26:02.187517 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2026-04-29 16:26:02.285742 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2026-04-29 16:26:02.380388 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2026-04-29 16:26:02.477241 INFO::Fitting model to feature number 82, Escherichia.coli
## 2026-04-29 16:26:02.570929 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2026-04-29 16:26:02.663262 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae

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

## 2026-04-29 16:26:02.749614 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae

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

## 2026-04-29 16:26:02.838876 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2026-04-29 16:26:02.933116 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2026-04-29 16:26:03.064137 INFO::Counting total values for each feature
## 2026-04-29 16:26:03.084776 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2026-04-29 16:26:03.149625 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2026-04-29 16:26:03.21524 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2026-04-29 16:26:03.307836 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2026-04-29 16:26:03.345801 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2026-04-29 16:26:03.36797 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2026-04-29 16:26:03.371586 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2026-04-29 16:26:03.374903 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
## 2026-04-29 16:26:03.376517 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2026-04-29 16:26:03.509086 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2026-04-29 16:26:03.513231 INFO::Plotting associations from most to least significant, grouped by metadata
## 2026-04-29 16:26:03.513934 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2026-04-29 16:26:03.515048 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii

## 2026-04-29 16:26:03.824213 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified

## 2026-04-29 16:26:04.082039 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis

## 2026-04-29 16:26:04.334616 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale

## 2026-04-29 16:26:04.580469 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus

## 2026-04-29 16:26:04.826011 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus

## 2026-04-29 16:26:05.06683 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum

## 2026-04-29 16:26:05.308795 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified

## 2026-04-29 16:26:05.555409 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans

## 2026-04-29 16:26:05.797635 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis

## 2026-04-29 16:26:06.040264 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron

## 2026-04-29 16:26:06.279724 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis

## 2026-04-29 16:26:06.52149 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis

## 2026-04-29 16:26:06.760126 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei

## 2026-04-29 16:26:07.041625 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii

## 2026-04-29 16:26:07.290364 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens

## 2026-04-29 16:26:07.533529 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum

## 2026-04-29 16:26:07.786283 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena

## 2026-04-29 16:26:08.030206 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae

## 2026-04-29 16:26:08.275354 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-04-29 16:26:08.519973 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli

## 2026-04-29 16:26:08.764328 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae

## 2026-04-29 16:26:09.007773 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified

## 2026-04-29 16:26:09.254012 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii

## 2026-04-29 16:26:09.49737 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens

## 2026-04-29 16:26:09.739818 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris

## 2026-04-29 16:26:09.984586 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes

## 2026-04-29 16:26:10.23601 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis

## 2026-04-29 16:26:10.478958 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii

## 2026-04-29 16:26:10.721492 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii

## 2026-04-29 16:26:10.967618 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis

## 2026-04-29 16:26:11.242598 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara

## 2026-04-29 16:26:11.489931 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum

## 2026-04-29 16:26:11.732066 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae

## 2026-04-29 16:26:11.98048 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified

## 2026-04-29 16:26:12.244272 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens

## 2026-04-29 16:26:12.492275 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus

## 2026-04-29 16:26:12.744989 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme

## 2026-04-29 16:26:13.000949 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii

## 2026-04-29 16:26:13.248457 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii

## 2026-04-29 16:26:13.501527 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum

## 2026-04-29 16:26:13.759384 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris

## 2026-04-29 16:26:14.024724 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47

## 2026-04-29 16:26:14.276021 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus

## 2026-04-29 16:26:14.552263 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii

## 2026-04-29 16:26:14.808653 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis

## 2026-04-29 16:26:15.079189 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified

## 2026-04-29 16:26:15.336658 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques

## 2026-04-29 16:26:15.61572 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified

## 2026-04-29 16:26:15.882258 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus

## 2026-04-29 16:26:16.139069 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis

## 2026-04-29 16:26:16.408171 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified

## 2026-04-29 16:26:16.678588 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified

## 2026-04-29 16:26:16.937985 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis

## 2026-04-29 16:26:17.191397 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis

## 2026-04-29 16:26:17.450599 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31

## 2026-04-29 16:26:17.711287 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae

## 2026-04-29 16:26:17.972756 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8

## 2026-04-29 16:26:18.223313 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae

## 2026-04-29 16:26:18.480273 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii

## 2026-04-29 16:26:18.744633 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii

## 2026-04-29 16:26:19.006796 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum

## 2026-04-29 16:26:19.256892 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA

## 2026-04-29 16:26:21.918708 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2026-04-29 16:26:21.919984 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified

## 2026-04-29 16:26:22.159172 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii

## 2026-04-29 16:26:22.423811 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae

## 2026-04-29 16:26:22.693675 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified

## 2026-04-29 16:26:22.964575 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis

## 2026-04-29 16:26:23.233815 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum

## 2026-04-29 16:26:23.499234 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus

## 2026-04-29 16:26:23.757617 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis

## 2026-04-29 16:26:24.036677 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii

## 2026-04-29 16:26:24.299989 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale

## 2026-04-29 16:26:24.561288 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis

## 2026-04-29 16:26:24.840055 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis

## 2026-04-29 16:26:25.140788 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-04-29 16:26:25.406464 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii

## 2026-04-29 16:26:25.680011 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens

## 2026-04-29 16:26:25.976404 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris

## 2026-04-29 16:26:26.254953 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii

## 2026-04-29 16:26:26.53608 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis

## 2026-04-29 16:26:26.829934 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum

## 2026-04-29 16:26:27.101135 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus

## 2026-04-29 16:26:27.391182 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii

## 2026-04-29 16:26:27.681264 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii

## 2026-04-29 16:26:27.958305 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae

## 2026-04-29 16:26:28.248884 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus

## 2026-04-29 16:26:28.524767 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum

## 2026-04-29 16:26:28.813767 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae

## 2026-04-29 16:26:29.098155 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae

## 2026-04-29 16:26:29.60674 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum

## 2026-04-29 16:26:29.84481 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis

## 2026-04-29 16:26:30.085409 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii

## 2026-04-29 16:26:30.337453 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques

## 2026-04-29 16:26:30.584362 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8

## 2026-04-29 16:26:30.838369 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum

## 2026-04-29 16:26:31.073405 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum

## 2026-04-29 16:26:31.320117 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis

## 2026-04-29 16:26:31.551224 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens

## 2026-04-29 16:26:31.78642 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi

## 2026-04-29 16:26:32.028241 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified

## 2026-04-29 16:26:32.268721 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens

## 2026-04-29 16:26:32.505722 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus

## 2026-04-29 16:26:32.743591 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae

## 2026-04-29 16:26:32.989042 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus

## 2026-04-29 16:26:33.23088 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris

## 2026-04-29 16:26:33.469527 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47

## 2026-04-29 16:26:36.003599 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2026-04-29 16:26:36.004927 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii

## 2026-04-29 16:26:36.235089 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale

## 2026-04-29 16:26:36.488912 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31

## 2026-04-29 16:26:36.740752 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis

## 2026-04-29 16:26:36.982943 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified

## 2026-04-29 16:26:37.233094 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-04-29 16:26:37.497284 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques

## 2026-04-29 16:26:37.748848 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum

## 2026-04-29 16:26:38.003245 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus

## 2026-04-29 16:26:38.257744 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli

## 2026-04-29 16:26:38.509252 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum

## 2026-04-29 16:26:38.790498 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified

## 2026-04-29 16:26:39.047595 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis

## 2026-04-29 16:26:39.310314 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens

## 2026-04-29 16:26:39.567706 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae

## 2026-04-29 16:26:39.820852 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii

## 2026-04-29 16:26:40.070395 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus

## 2026-04-29 16:26:40.324004 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified

## 2026-04-29 16:26:40.578843 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis

## 2026-04-29 16:26:40.833028 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii

## 2026-04-29 16:26:41.081949 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans

## 2026-04-29 16:26:41.33012 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii

## 2026-04-29 16:26:41.593671 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified

## 2026-04-29 16:26:41.843154 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii

## 2026-04-29 16:26:42.103084 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis

## 2026-04-29 16:26:42.364218 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri

## 2026-04-29 16:26:42.651747 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei

## 2026-04-29 16:26:42.907833 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis

## 2026-04-29 16:26:43.180563 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii

## 2026-04-29 16:26:45.822672 INFO::Plotting data for metadata number 4, antibiotics
## 2026-04-29 16:26:45.82403 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans

## 2026-04-29 16:26:46.058033 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis

## 2026-04-29 16:26:46.321962 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale

## 2026-04-29 16:26:46.573836 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus

## 2026-04-29 16:26:46.837964 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis

## 2026-04-29 16:26:47.094276 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena

## 2026-04-29 16:26:47.378481 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus

## 2026-04-29 16:26:47.646692 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii

## 2026-04-29 16:26:47.903447 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum

## 2026-04-29 16:26:48.155524 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae

## 2026-04-29 16:26:48.422409 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis

## 2026-04-29 16:26:48.678861 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii

## 2026-04-29 16:26:48.929381 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii

## 2026-04-29 16:26:49.201302 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified

## 2026-04-29 16:26:49.456544 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum

## 2026-04-29 16:26:49.72022 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-04-29 16:26:49.977804 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii

## 2026-04-29 16:26:50.243082 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31

## 2026-04-29 16:26:50.491636 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis

## 2026-04-29 16:26:50.75278 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii

## 2026-04-29 16:26:51.037525 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis

## 2026-04-29 16:26:51.310681 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens

## 2026-04-29 16:26:51.564459 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens

## 2026-04-29 16:26:51.836468 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron

## 2026-04-29 16:26:52.101661 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii

## 2026-04-29 16:26:52.37007 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae

## 2026-04-29 16:26:52.636149 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum

## 2026-04-29 16:26:52.902478 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques

## 2026-04-29 16:26:53.171564 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum

## 2026-04-29 16:26:53.463711 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis

## 2026-04-29 16:26:53.732321 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified

## 2026-04-29 16:26:54.010576 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar

## 2026-04-29 16:26:54.278113 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica

## 2026-04-29 16:26:54.540784 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8

## 2026-04-29 16:26:55.067056 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile

## 2026-04-29 16:26:55.292633 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47

## 2026-04-29 16:26:55.513379 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA

## 2026-04-29 16:26:55.738508 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila

## 2026-04-29 16:26:55.961869 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae

## 2026-04-29 16:26:56.18647 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus

## 2026-04-29 16:26:58.491409 INFO::Plotting data for metadata number 5, age
## 2026-04-29 16:26:58.492657 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()`).

## 2026-04-29 16:26:58.752468 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()`).

## 2026-04-29 16:26:59.030465 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()`).

## 2026-04-29 16:26:59.243904 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()`).

## 2026-04-29 16:26:59.466234 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()`).

## 2026-04-29 16:26:59.70476 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()`).

## 2026-04-29 16:26:59.923876 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()`).

## 2026-04-29 16:27:00.160482 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()`).

## 2026-04-29 16:27:00.389075 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()`).

## 2026-04-29 16:27:00.611153 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()`).

## 2026-04-29 16:27:00.831167 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()`).

## 2026-04-29 16:27:01.04658 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()`).

## 2026-04-29 16:27:01.275435 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()`).

## 2026-04-29 16:27:01.497951 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()`).

## 2026-04-29 16:27:01.713777 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()`).

## 2026-04-29 16:27:01.936654 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()`).

## 2026-04-29 16:27:02.153957 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()`).

## 2026-04-29 16:27:02.373002 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()`).

## 2026-04-29 16:27:02.589826 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()`).

## 2026-04-29 16:27:02.805988 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()`).

## 2026-04-29 16:27:03.036133 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()`).

## 2026-04-29 16:27:03.300547 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()`).

## 2026-04-29 16:27:05.80708 INFO::Plotting data for metadata number 6, diagnosis
## 2026-04-29 16:27:05.808506 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis

## 2026-04-29 16:27:06.044987 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila

## 2026-04-29 16:27:06.305519 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae

## 2026-04-29 16:27:06.584989 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis

## 2026-04-29 16:27:06.845128 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified

## 2026-04-29 16:27:07.113819 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme

## 2026-04-29 16:27:07.394791 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii

## 2026-04-29 16:27:07.694238 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii

## 2026-04-29 16:27:07.95992 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum

## 2026-04-29 16:27:08.23673 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum

## 2026-04-29 16:27:08.500239 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans

## 2026-04-29 16:27:08.785312 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii

## 2026-04-29 16:27:09.048719 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii

## 2026-04-29 16:27:09.325769 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii

## 2026-04-29 16:27:09.592608 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii

## 2026-04-29 16:27:09.873178 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified

## 2026-04-29 16:27:10.141661 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum

## 2026-04-29 16:27:10.409146 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis

## 2026-04-29 16:27:10.69223 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified

## 2026-04-29 16:27:10.97075 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii

## 2026-04-29 16:27:11.271816 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum

## 2026-04-29 16:27:11.542824 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis

## 2026-04-29 16:27:11.841005 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis

## 2026-04-29 16:27:12.114053 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila

## 2026-04-29 16:27:12.394561 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis

## 2026-04-29 16:27:12.657807 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified

## 2026-04-29 16:27:12.936544 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum

## 2026-04-29 16:27:13.22539 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii

## 2026-04-29 16:27:13.49937 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified

## 2026-04-29 16:27:13.775384 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris

## 2026-04-29 16:27:14.058899 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus

## 2026-04-29 16:27:14.335226 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus

## 2026-04-29 16:27:14.613942 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis

## 2026-04-29 16:27:14.921038 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale

## 2026-04-29 16:27:15.212433 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus

## 2026-04-29 16:27:15.504058 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis

## 2026-04-29 16:27:15.780037 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale

## 2026-04-29 16:27:16.077734 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii

## 2026-04-29 16:27:16.363002 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus

## 2026-04-29 16:27:16.641205 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii

## 2026-04-29 16:27:16.929811 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis

## 2026-04-29 16:27:17.222939 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae

## 2026-04-29 16:27:17.509133 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_0.10.0        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_0.10-108    pheatmap_1.0.13    
## [19] Matrix_1.7-5        data.table_1.18.2.1 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_2.7-3         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