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 05:02:21.091819 INFO::Writing function arguments to log file
## 2026-07-04 05:02:21.18101 INFO::Verifying options selected are valid
## 2026-07-04 05:02:21.203576 INFO::Determining format of input files
## 2026-07-04 05:02:21.204555 INFO::Input format is data samples as rows and metadata samples as rows
## 2026-07-04 05:02:21.207978 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2026-07-04 05:02:21.208836 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2026-07-04 05:02:21.210583 INFO::Filter data based on min abundance and min prevalence
## 2026-07-04 05:02:21.211133 INFO::Total samples in data: 1595
## 2026-07-04 05:02:21.211689 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2026-07-04 05:02:21.21541 INFO::Total filtered features: 0
## 2026-07-04 05:02:21.216225 INFO::Filtered feature names from abundance and prevalence filtering:
## 2026-07-04 05:02:21.222959 INFO::Total filtered features with variance filtering: 0
## 2026-07-04 05:02:21.22379 INFO::Filtered feature names from variance filtering:
## 2026-07-04 05:02:21.224329 INFO::Running selected normalization method: TSS
## 2026-07-04 05:02:22.029788 INFO::Bypass z-score application to metadata
## 2026-07-04 05:02:22.030757 INFO::Running selected transform method: LOG
## 2026-07-04 05:02:22.052918 INFO::Running selected analysis method: LM
## 2026-07-04 05:02:22.290429 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis

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

## 2026-07-04 05:02:22.698925 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2026-07-04 05:02:22.801937 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2026-07-04 05:02:22.958177 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum

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

## 2026-07-04 05:02:23.050149 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2026-07-04 05:02:23.161374 INFO::Fitting model to feature number 6, Bacteroides.caccae

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

## 2026-07-04 05:02:23.255749 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2026-07-04 05:02:23.359943 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2026-07-04 05:02:23.46169 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2026-07-04 05:02:23.565383 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2026-07-04 05:02:23.664878 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 05:02:23.749154 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 05:02:23.851525 INFO::Fitting model to feature number 12, Bacteroides.fragilis

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

## 2026-07-04 05:02:23.945432 INFO::Fitting model to feature number 13, Bacteroides.intestinalis

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

## 2026-07-04 05:02:24.048494 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2026-07-04 05:02:24.144645 INFO::Fitting model to feature number 15, Bacteroides.ovatus

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

## 2026-07-04 05:02:24.24035 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2026-07-04 05:02:24.343399 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2026-07-04 05:02:24.446433 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron

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

## 2026-07-04 05:02:24.543254 INFO::Fitting model to feature number 19, Bacteroides.uniformis

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

## 2026-07-04 05:02:24.641781 INFO::Fitting model to feature number 20, Bacteroides.vulgatus

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

## 2026-07-04 05:02:24.747341 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens

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

## 2026-07-04 05:02:24.842385 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2026-07-04 05:02:24.944941 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2026-07-04 05:02:25.043571 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2026-07-04 05:02:25.151688 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2026-07-04 05:02:25.248983 INFO::Fitting model to feature number 26, Parabacteroides.distasonis

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

## 2026-07-04 05:02:25.349242 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2026-07-04 05:02:25.455251 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2026-07-04 05:02:25.554014 INFO::Fitting model to feature number 29, Parabacteroides.unclassified

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

## 2026-07-04 05:02:25.65359 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2026-07-04 05:02:25.753018 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2026-07-04 05:02:25.855976 INFO::Fitting model to feature number 32, Prevotella.copri

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

## 2026-07-04 05:02:25.955393 INFO::Fitting model to feature number 33, Alistipes.finegoldii

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

## 2026-07-04 05:02:26.052921 INFO::Fitting model to feature number 34, Alistipes.onderdonkii

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

## 2026-07-04 05:02:26.149338 INFO::Fitting model to feature number 35, Alistipes.putredinis

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

## 2026-07-04 05:02:26.438553 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2026-07-04 05:02:26.53541 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2026-07-04 05:02:26.634031 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2026-07-04 05:02:26.742186 INFO::Fitting model to feature number 39, Clostridium.bolteae

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

## 2026-07-04 05:02:26.835638 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 05:02:26.912281 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 05:02:27.012421 INFO::Fitting model to feature number 41, Clostridium.clostridioforme

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

## 2026-07-04 05:02:27.103252 INFO::Fitting model to feature number 42, Clostridium.hathewayi

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

## 2026-07-04 05:02:27.196846 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2026-07-04 05:02:27.310433 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2026-07-04 05:02:27.402644 INFO::Fitting model to feature number 45, Clostridium.symbiosum

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

## 2026-07-04 05:02:27.494024 INFO::Fitting model to feature number 46, Flavonifractor.plautii

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

## 2026-07-04 05:02:27.598759 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2026-07-04 05:02:27.693793 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2026-07-04 05:02:27.792138 INFO::Fitting model to feature number 49, Eubacterium.rectale

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

## 2026-07-04 05:02:27.889506 INFO::Fitting model to feature number 50, Eubacterium.siraeum

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

## 2026-07-04 05:02:27.986155 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31

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

## 2026-07-04 05:02:28.078388 INFO::Fitting model to feature number 52, Eubacterium.ventriosum

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

## 2026-07-04 05:02:28.166996 INFO::Fitting model to feature number 53, Ruminococcus.gnavus

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

## 2026-07-04 05:02:28.457323 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2026-07-04 05:02:28.550081 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2026-07-04 05:02:28.643289 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2026-07-04 05:02:28.749051 INFO::Fitting model to feature number 57, Dorea.longicatena

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

## 2026-07-04 05:02:28.864264 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA

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

## 2026-07-04 05:02:28.95931 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA

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

## 2026-07-04 05:02:29.05363 INFO::Fitting model to feature number 60, Roseburia.hominis

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

## 2026-07-04 05:02:29.148148 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2026-07-04 05:02:29.23924 INFO::Fitting model to feature number 62, Roseburia.inulinivorans

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

## 2026-07-04 05:02:29.337829 INFO::Fitting model to feature number 63, Roseburia.unclassified

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

## 2026-07-04 05:02:29.431315 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2026-07-04 05:02:29.531858 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2026-07-04 05:02:29.630261 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2026-07-04 05:02:29.724945 INFO::Fitting model to feature number 67, Ruminococcus.bromii

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

## 2026-07-04 05:02:29.817866 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2026-07-04 05:02:29.910151 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2026-07-04 05:02:30.006706 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified

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

## 2026-07-04 05:02:30.102243 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2026-07-04 05:02:30.202392 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2026-07-04 05:02:30.300773 INFO::Fitting model to feature number 73, Dialister.invisus

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

## 2026-07-04 05:02:30.390751 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2026-07-04 05:02:30.487988 INFO::Fitting model to feature number 75, Veillonella.dispar

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

## 2026-07-04 05:02:30.588225 INFO::Fitting model to feature number 76, Veillonella.parvula

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

## 2026-07-04 05:02:30.678737 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2026-07-04 05:02:30.77295 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2026-07-04 05:02:30.870492 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2026-07-04 05:02:30.970683 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2026-07-04 05:02:31.069259 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2026-07-04 05:02:31.171942 INFO::Fitting model to feature number 82, Escherichia.coli
## 2026-07-04 05:02:31.269109 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2026-07-04 05:02:31.566713 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae

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

## 2026-07-04 05:02:31.657614 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae

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

## 2026-07-04 05:02:31.754548 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2026-07-04 05:02:31.855977 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2026-07-04 05:02:31.988285 INFO::Counting total values for each feature
## 2026-07-04 05:02:32.009351 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2026-07-04 05:02:32.071828 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2026-07-04 05:02:32.133885 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2026-07-04 05:02:32.222709 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2026-07-04 05:02:32.261417 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2026-07-04 05:02:32.28372 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2026-07-04 05:02:32.287489 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2026-07-04 05:02:32.290808 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 05:02:32.292439 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2026-07-04 05:02:32.697392 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2026-07-04 05:02:32.701399 INFO::Plotting associations from most to least significant, grouped by metadata
## 2026-07-04 05:02:32.702059 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2026-07-04 05:02:32.703254 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii

## 2026-07-04 05:02:33.029683 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified

## 2026-07-04 05:02:33.308633 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis

## 2026-07-04 05:02:33.578332 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale

## 2026-07-04 05:02:33.850466 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus

## 2026-07-04 05:02:34.113816 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus

## 2026-07-04 05:02:34.374239 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum

## 2026-07-04 05:02:34.639373 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified

## 2026-07-04 05:02:34.912084 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans

## 2026-07-04 05:02:35.186521 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis

## 2026-07-04 05:02:35.467657 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron

## 2026-07-04 05:02:35.777683 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis

## 2026-07-04 05:02:36.044455 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis

## 2026-07-04 05:02:36.311072 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei

## 2026-07-04 05:02:36.585773 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii

## 2026-07-04 05:02:36.854955 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens

## 2026-07-04 05:02:37.12198 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum

## 2026-07-04 05:02:37.393756 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena

## 2026-07-04 05:02:37.67228 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae

## 2026-07-04 05:02:37.945353 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-07-04 05:02:38.21446 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli

## 2026-07-04 05:02:38.482533 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae

## 2026-07-04 05:02:38.75683 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified

## 2026-07-04 05:02:39.012177 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii

## 2026-07-04 05:02:39.277015 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens

## 2026-07-04 05:02:39.546192 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris

## 2026-07-04 05:02:39.817063 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes

## 2026-07-04 05:02:40.090257 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis

## 2026-07-04 05:02:40.40029 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii

## 2026-07-04 05:02:40.676417 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii

## 2026-07-04 05:02:40.951049 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis

## 2026-07-04 05:02:41.224409 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara

## 2026-07-04 05:02:41.499142 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum

## 2026-07-04 05:02:41.768234 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae

## 2026-07-04 05:02:42.041697 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified

## 2026-07-04 05:02:42.323969 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens

## 2026-07-04 05:02:42.593427 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus

## 2026-07-04 05:02:42.869702 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme

## 2026-07-04 05:02:43.141861 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii

## 2026-07-04 05:02:43.427051 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii

## 2026-07-04 05:02:43.69818 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum

## 2026-07-04 05:02:43.972429 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris

## 2026-07-04 05:02:44.254584 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47

## 2026-07-04 05:02:44.519013 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus

## 2026-07-04 05:02:44.800989 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii

## 2026-07-04 05:02:45.117901 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis

## 2026-07-04 05:02:45.397596 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified

## 2026-07-04 05:02:45.681765 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques

## 2026-07-04 05:02:45.957726 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified

## 2026-07-04 05:02:46.249966 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus

## 2026-07-04 05:02:46.545734 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis

## 2026-07-04 05:02:46.833968 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified

## 2026-07-04 05:02:47.124856 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified

## 2026-07-04 05:02:47.412767 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis

## 2026-07-04 05:02:47.70401 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis

## 2026-07-04 05:02:47.994092 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31

## 2026-07-04 05:02:48.275631 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae

## 2026-07-04 05:02:48.553316 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8

## 2026-07-04 05:02:48.852584 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae

## 2026-07-04 05:02:49.131223 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii

## 2026-07-04 05:02:49.423202 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii

## 2026-07-04 05:02:49.717026 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum

## 2026-07-04 05:02:50.036343 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA

## 2026-07-04 05:02:52.937705 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2026-07-04 05:02:52.939524 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified

## 2026-07-04 05:02:53.215848 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii

## 2026-07-04 05:02:53.511646 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae

## 2026-07-04 05:02:53.804616 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified

## 2026-07-04 05:02:54.097544 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis

## 2026-07-04 05:02:54.410279 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum

## 2026-07-04 05:02:54.709873 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus

## 2026-07-04 05:02:54.998954 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis

## 2026-07-04 05:02:55.305374 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii

## 2026-07-04 05:02:55.844995 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale

## 2026-07-04 05:02:56.101373 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis

## 2026-07-04 05:02:56.362795 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis

## 2026-07-04 05:02:56.619036 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-07-04 05:02:56.874637 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii

## 2026-07-04 05:02:57.133281 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens

## 2026-07-04 05:02:57.392078 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris

## 2026-07-04 05:02:57.656915 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii

## 2026-07-04 05:02:57.91638 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis

## 2026-07-04 05:02:58.170884 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum

## 2026-07-04 05:02:58.422142 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus

## 2026-07-04 05:02:58.680215 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii

## 2026-07-04 05:02:58.94635 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii

## 2026-07-04 05:02:59.202631 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae

## 2026-07-04 05:02:59.459401 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus

## 2026-07-04 05:02:59.718911 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum

## 2026-07-04 05:02:59.977376 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae

## 2026-07-04 05:03:00.236845 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae

## 2026-07-04 05:03:00.5289 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum

## 2026-07-04 05:03:00.794985 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis

## 2026-07-04 05:03:01.076521 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii

## 2026-07-04 05:03:01.351746 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques

## 2026-07-04 05:03:01.617266 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8

## 2026-07-04 05:03:01.894248 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum

## 2026-07-04 05:03:02.16541 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum

## 2026-07-04 05:03:02.441718 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis

## 2026-07-04 05:03:02.71617 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens

## 2026-07-04 05:03:02.987817 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi

## 2026-07-04 05:03:03.256361 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified

## 2026-07-04 05:03:03.519626 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens

## 2026-07-04 05:03:03.798215 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus

## 2026-07-04 05:03:04.066716 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae

## 2026-07-04 05:03:04.336644 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus

## 2026-07-04 05:03:04.614295 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris

## 2026-07-04 05:03:04.884091 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47

## 2026-07-04 05:03:07.653734 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2026-07-04 05:03:07.65518 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii

## 2026-07-04 05:03:07.906085 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale

## 2026-07-04 05:03:08.183048 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31

## 2026-07-04 05:03:08.475545 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis

## 2026-07-04 05:03:08.755529 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified

## 2026-07-04 05:03:09.03292 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-07-04 05:03:09.313542 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques

## 2026-07-04 05:03:09.589873 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum

## 2026-07-04 05:03:09.895334 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus

## 2026-07-04 05:03:10.175727 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli

## 2026-07-04 05:03:10.45099 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum

## 2026-07-04 05:03:10.776886 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified

## 2026-07-04 05:03:11.071662 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis

## 2026-07-04 05:03:11.350629 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens

## 2026-07-04 05:03:11.632599 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae

## 2026-07-04 05:03:11.91957 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii

## 2026-07-04 05:03:12.198566 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus

## 2026-07-04 05:03:12.474812 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified

## 2026-07-04 05:03:12.765063 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis

## 2026-07-04 05:03:13.039308 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii

## 2026-07-04 05:03:13.307965 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans

## 2026-07-04 05:03:13.604125 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii

## 2026-07-04 05:03:13.884516 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified

## 2026-07-04 05:03:14.174931 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii

## 2026-07-04 05:03:14.446095 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis

## 2026-07-04 05:03:14.73925 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri

## 2026-07-04 05:03:15.052635 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei

## 2026-07-04 05:03:15.340915 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis

## 2026-07-04 05:03:15.639178 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii

## 2026-07-04 05:03:18.52278 INFO::Plotting data for metadata number 4, antibiotics
## 2026-07-04 05:03:18.524248 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans

## 2026-07-04 05:03:18.793769 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis

## 2026-07-04 05:03:19.07864 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale

## 2026-07-04 05:03:19.353675 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus

## 2026-07-04 05:03:19.654396 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis

## 2026-07-04 05:03:19.930982 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena

## 2026-07-04 05:03:20.249181 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus

## 2026-07-04 05:03:20.556639 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii

## 2026-07-04 05:03:20.836243 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum

## 2026-07-04 05:03:21.117253 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae

## 2026-07-04 05:03:21.413049 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis

## 2026-07-04 05:03:21.688938 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii

## 2026-07-04 05:03:21.961448 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii

## 2026-07-04 05:03:22.255161 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified

## 2026-07-04 05:03:22.533102 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum

## 2026-07-04 05:03:22.819538 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-07-04 05:03:23.09826 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii

## 2026-07-04 05:03:23.384742 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31

## 2026-07-04 05:03:23.659127 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis

## 2026-07-04 05:03:23.94257 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii

## 2026-07-04 05:03:24.486577 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis

## 2026-07-04 05:03:24.723752 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens

## 2026-07-04 05:03:24.954932 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens

## 2026-07-04 05:03:25.191263 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron

## 2026-07-04 05:03:25.42686 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii

## 2026-07-04 05:03:25.664541 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae

## 2026-07-04 05:03:25.894729 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum

## 2026-07-04 05:03:26.131351 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques

## 2026-07-04 05:03:26.361131 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum

## 2026-07-04 05:03:26.600028 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis

## 2026-07-04 05:03:26.837486 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified

## 2026-07-04 05:03:27.073342 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar

## 2026-07-04 05:03:27.306526 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica

## 2026-07-04 05:03:27.539606 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8

## 2026-07-04 05:03:27.77399 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile

## 2026-07-04 05:03:28.012136 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47

## 2026-07-04 05:03:28.242697 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA

## 2026-07-04 05:03:28.478502 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila

## 2026-07-04 05:03:28.754855 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae

## 2026-07-04 05:03:29.004499 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus

## 2026-07-04 05:03:31.474735 INFO::Plotting data for metadata number 5, age
## 2026-07-04 05:03:31.476084 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 05:03:31.766744 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 05:03:32.065381 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 05:03:32.300735 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 05:03:32.539629 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 05:03:32.769231 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 05:03:33.000129 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 05:03:33.251387 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 05:03:33.48721 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 05:03:33.755729 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 05:03:34.002114 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 05:03:34.242381 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 05:03:34.481797 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 05:03:34.726744 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 05:03:34.980736 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 05:03:35.215245 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 05:03:35.45158 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 05:03:35.698983 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 05:03:35.929567 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 05:03:36.178001 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 05:03:36.418211 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 05:03:36.669366 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 05:03:39.252706 INFO::Plotting data for metadata number 6, diagnosis
## 2026-07-04 05:03:39.254293 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis

## 2026-07-04 05:03:39.507516 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila

## 2026-07-04 05:03:39.788897 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae

## 2026-07-04 05:03:40.078006 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis

## 2026-07-04 05:03:40.356531 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified

## 2026-07-04 05:03:40.649334 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme

## 2026-07-04 05:03:40.920191 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii

## 2026-07-04 05:03:41.207638 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii

## 2026-07-04 05:03:41.479887 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum

## 2026-07-04 05:03:41.769797 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum

## 2026-07-04 05:03:42.083445 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans

## 2026-07-04 05:03:42.368525 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii

## 2026-07-04 05:03:42.667375 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii

## 2026-07-04 05:03:42.946449 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii

## 2026-07-04 05:03:43.235915 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii

## 2026-07-04 05:03:43.514112 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified

## 2026-07-04 05:03:43.802658 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum

## 2026-07-04 05:03:44.097528 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis

## 2026-07-04 05:03:44.388945 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified

## 2026-07-04 05:03:44.6718 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii

## 2026-07-04 05:03:44.957683 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum

## 2026-07-04 05:03:45.247488 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis

## 2026-07-04 05:03:45.566149 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis

## 2026-07-04 05:03:45.859806 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila

## 2026-07-04 05:03:46.148066 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis

## 2026-07-04 05:03:46.443552 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified

## 2026-07-04 05:03:46.731205 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum

## 2026-07-04 05:03:47.042982 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii

## 2026-07-04 05:03:47.35162 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified

## 2026-07-04 05:03:47.647583 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris

## 2026-07-04 05:03:47.9434 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus

## 2026-07-04 05:03:48.256111 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus

## 2026-07-04 05:03:48.553289 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis

## 2026-07-04 05:03:48.856874 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale

## 2026-07-04 05:03:49.385276 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus

## 2026-07-04 05:03:49.649099 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis

## 2026-07-04 05:03:49.896833 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale

## 2026-07-04 05:03:50.144392 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii

## 2026-07-04 05:03:50.395841 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus

## 2026-07-04 05:03:50.639852 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii

## 2026-07-04 05:03:50.883311 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis

## 2026-07-04 05:03:51.137032 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae

## 2026-07-04 05:03:51.384626 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_1.27.0
## 
## 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