MaAsLin2 User Manual

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

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

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

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

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

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

Description
Requirements
Installation
How to Run
Visualization
Troubleshooting

Description

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

Requirements

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

Installation

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

From command line

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

From R

Install Bioconductor and then install Maaslin2

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

How to Run

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

Input Files

MaAsLin2 requires two input files.

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

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

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

Output Files

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

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

Run a Demo

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

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

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

Command line

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

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

In R

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

## [1] "Creating output folder"
## [1] "Creating output feature tables folder"
## [1] "Creating output fits folder"
## [1] "Creating output figures folder"
## 2026-05-30 07:46:51.407992 INFO::Writing function arguments to log file
## 2026-05-30 07:46:51.506272 INFO::Verifying options selected are valid
## 2026-05-30 07:46:51.526999 INFO::Determining format of input files
## 2026-05-30 07:46:51.527832 INFO::Input format is data samples as rows and metadata samples as rows
## 2026-05-30 07:46:51.531665 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2026-05-30 07:46:51.532462 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2026-05-30 07:46:51.534023 INFO::Filter data based on min abundance and min prevalence
## 2026-05-30 07:46:51.534544 INFO::Total samples in data: 1595
## 2026-05-30 07:46:51.535005 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2026-05-30 07:46:51.539364 INFO::Total filtered features: 0
## 2026-05-30 07:46:51.540075 INFO::Filtered feature names from abundance and prevalence filtering:
## 2026-05-30 07:46:51.547412 INFO::Total filtered features with variance filtering: 0
## 2026-05-30 07:46:51.548077 INFO::Filtered feature names from variance filtering:
## 2026-05-30 07:46:51.548624 INFO::Running selected normalization method: TSS
## 2026-05-30 07:46:52.369792 INFO::Bypass z-score application to metadata
## 2026-05-30 07:46:52.370721 INFO::Running selected transform method: LOG
## 2026-05-30 07:46:52.394459 INFO::Running selected analysis method: LM
## 2026-05-30 07:46:52.615604 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis

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

## 2026-05-30 07:46:53.261503 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2026-05-30 07:46:53.361329 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2026-05-30 07:46:53.453945 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum

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

## 2026-05-30 07:46:53.549837 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2026-05-30 07:46:53.651085 INFO::Fitting model to feature number 6, Bacteroides.caccae

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

## 2026-05-30 07:46:53.75859 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2026-05-30 07:46:53.852784 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2026-05-30 07:46:53.952751 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2026-05-30 07:46:54.055697 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2026-05-30 07:46:54.151515 INFO::Fitting model to feature number 11, Bacteroides.finegoldii

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

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

## 2026-05-30 07:46:54.228986 WARNING::Fitting problem for feature 11 a warning was issued

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

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

## 2026-05-30 07:46:54.329774 INFO::Fitting model to feature number 12, Bacteroides.fragilis

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

## 2026-05-30 07:46:54.420635 INFO::Fitting model to feature number 13, Bacteroides.intestinalis

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

## 2026-05-30 07:46:54.524434 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2026-05-30 07:46:54.616872 INFO::Fitting model to feature number 15, Bacteroides.ovatus

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

## 2026-05-30 07:46:54.70343 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2026-05-30 07:46:54.803393 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2026-05-30 07:46:54.896784 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron

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

## 2026-05-30 07:46:54.992221 INFO::Fitting model to feature number 19, Bacteroides.uniformis

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

## 2026-05-30 07:46:55.086419 INFO::Fitting model to feature number 20, Bacteroides.vulgatus

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

## 2026-05-30 07:46:55.181985 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens

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

## 2026-05-30 07:46:55.285362 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2026-05-30 07:46:55.381271 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2026-05-30 07:46:55.479512 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2026-05-30 07:46:55.588856 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2026-05-30 07:46:55.684094 INFO::Fitting model to feature number 26, Parabacteroides.distasonis

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

## 2026-05-30 07:46:55.783901 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2026-05-30 07:46:55.880456 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2026-05-30 07:46:55.978316 INFO::Fitting model to feature number 29, Parabacteroides.unclassified

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

## 2026-05-30 07:46:56.075631 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2026-05-30 07:46:56.172637 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2026-05-30 07:46:56.276506 INFO::Fitting model to feature number 32, Prevotella.copri

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

## 2026-05-30 07:46:56.367254 INFO::Fitting model to feature number 33, Alistipes.finegoldii

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

## 2026-05-30 07:46:56.458314 INFO::Fitting model to feature number 34, Alistipes.onderdonkii

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

## 2026-05-30 07:46:56.556979 INFO::Fitting model to feature number 35, Alistipes.putredinis

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

## 2026-05-30 07:46:56.648582 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2026-05-30 07:46:56.753347 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2026-05-30 07:46:56.846548 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2026-05-30 07:46:56.949659 INFO::Fitting model to feature number 39, Clostridium.bolteae

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

## 2026-05-30 07:46:57.045281 INFO::Fitting model to feature number 40, Clostridium.citroniae

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

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

## 2026-05-30 07:46:57.130468 WARNING::Fitting problem for feature 40 a warning was issued

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

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

## 2026-05-30 07:46:57.224267 INFO::Fitting model to feature number 41, Clostridium.clostridioforme

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

## 2026-05-30 07:46:57.326256 INFO::Fitting model to feature number 42, Clostridium.hathewayi

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

## 2026-05-30 07:46:57.436999 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2026-05-30 07:46:57.548358 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2026-05-30 07:46:57.642658 INFO::Fitting model to feature number 45, Clostridium.symbiosum

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

## 2026-05-30 07:46:57.743713 INFO::Fitting model to feature number 46, Flavonifractor.plautii

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

## 2026-05-30 07:46:57.846362 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2026-05-30 07:46:57.942041 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2026-05-30 07:46:58.058085 INFO::Fitting model to feature number 49, Eubacterium.rectale

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

## 2026-05-30 07:46:58.157722 INFO::Fitting model to feature number 50, Eubacterium.siraeum

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

## 2026-05-30 07:46:58.260634 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31

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

## 2026-05-30 07:46:58.356051 INFO::Fitting model to feature number 52, Eubacterium.ventriosum

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

## 2026-05-30 07:46:58.446112 INFO::Fitting model to feature number 53, Ruminococcus.gnavus

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

## 2026-05-30 07:46:58.551012 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2026-05-30 07:46:58.646469 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2026-05-30 07:46:59.000668 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2026-05-30 07:46:59.098316 INFO::Fitting model to feature number 57, Dorea.longicatena

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

## 2026-05-30 07:46:59.194042 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA

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

## 2026-05-30 07:46:59.297949 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA

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

## 2026-05-30 07:46:59.414099 INFO::Fitting model to feature number 60, Roseburia.hominis

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

## 2026-05-30 07:46:59.530363 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2026-05-30 07:46:59.623842 INFO::Fitting model to feature number 62, Roseburia.inulinivorans

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

## 2026-05-30 07:46:59.717659 INFO::Fitting model to feature number 63, Roseburia.unclassified

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

## 2026-05-30 07:46:59.812609 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2026-05-30 07:46:59.916647 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2026-05-30 07:47:00.02379 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2026-05-30 07:47:00.1218 INFO::Fitting model to feature number 67, Ruminococcus.bromii

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

## 2026-05-30 07:47:00.212422 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2026-05-30 07:47:00.30869 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2026-05-30 07:47:00.416481 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified

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

## 2026-05-30 07:47:00.510239 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2026-05-30 07:47:00.602805 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2026-05-30 07:47:00.703402 INFO::Fitting model to feature number 73, Dialister.invisus

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

## 2026-05-30 07:47:00.794333 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2026-05-30 07:47:00.900564 INFO::Fitting model to feature number 75, Veillonella.dispar

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

## 2026-05-30 07:47:00.994442 INFO::Fitting model to feature number 76, Veillonella.parvula

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

## 2026-05-30 07:47:01.087115 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2026-05-30 07:47:01.18068 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2026-05-30 07:47:01.287403 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2026-05-30 07:47:01.383956 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2026-05-30 07:47:01.482789 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2026-05-30 07:47:01.586753 INFO::Fitting model to feature number 82, Escherichia.coli
## 2026-05-30 07:47:01.685518 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2026-05-30 07:47:01.786966 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae

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

## 2026-05-30 07:47:01.882918 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae

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

## 2026-05-30 07:47:01.979136 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2026-05-30 07:47:02.078966 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2026-05-30 07:47:02.215069 INFO::Counting total values for each feature
## 2026-05-30 07:47:02.236522 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2026-05-30 07:47:02.298719 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2026-05-30 07:47:02.36075 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2026-05-30 07:47:02.448802 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2026-05-30 07:47:02.491093 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2026-05-30 07:47:02.51455 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2026-05-30 07:47:02.518312 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2026-05-30 07:47:02.52159 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): demo_output/significant_results.tsv
## 2026-05-30 07:47:02.523112 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2026-05-30 07:47:02.928995 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2026-05-30 07:47:02.933442 INFO::Plotting associations from most to least significant, grouped by metadata
## 2026-05-30 07:47:02.934127 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2026-05-30 07:47:02.935285 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii

## 2026-05-30 07:47:03.252995 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified

## 2026-05-30 07:47:03.520229 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis

## 2026-05-30 07:47:03.774385 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale

## 2026-05-30 07:47:04.026656 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus

## 2026-05-30 07:47:04.275676 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus

## 2026-05-30 07:47:04.523542 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum

## 2026-05-30 07:47:04.772196 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified

## 2026-05-30 07:47:05.031072 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans

## 2026-05-30 07:47:05.280091 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis

## 2026-05-30 07:47:05.525991 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron

## 2026-05-30 07:47:05.770597 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis

## 2026-05-30 07:47:06.017955 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis

## 2026-05-30 07:47:06.260996 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei

## 2026-05-30 07:47:06.567441 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii

## 2026-05-30 07:47:06.81589 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens

## 2026-05-30 07:47:07.075616 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum

## 2026-05-30 07:47:07.32947 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena

## 2026-05-30 07:47:07.580726 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae

## 2026-05-30 07:47:07.832981 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-05-30 07:47:08.084574 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli

## 2026-05-30 07:47:08.332591 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae

## 2026-05-30 07:47:08.584435 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified

## 2026-05-30 07:47:08.822459 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii

## 2026-05-30 07:47:09.066445 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens

## 2026-05-30 07:47:09.311835 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris

## 2026-05-30 07:47:09.566202 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes

## 2026-05-30 07:47:09.809265 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis

## 2026-05-30 07:47:10.052621 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii

## 2026-05-30 07:47:10.304515 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii

## 2026-05-30 07:47:10.543207 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis

## 2026-05-30 07:47:10.833652 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara

## 2026-05-30 07:47:11.089419 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum

## 2026-05-30 07:47:11.338447 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae

## 2026-05-30 07:47:11.599867 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified

## 2026-05-30 07:47:11.870714 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens

## 2026-05-30 07:47:12.126272 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus

## 2026-05-30 07:47:12.38562 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme

## 2026-05-30 07:47:12.645684 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii

## 2026-05-30 07:47:12.904018 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii

## 2026-05-30 07:47:13.172439 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum

## 2026-05-30 07:47:13.43912 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris

## 2026-05-30 07:47:13.695835 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47

## 2026-05-30 07:47:13.94737 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus

## 2026-05-30 07:47:14.224638 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii

## 2026-05-30 07:47:14.487809 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis

## 2026-05-30 07:47:14.744939 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified

## 2026-05-30 07:47:15.025627 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques

## 2026-05-30 07:47:15.32654 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified

## 2026-05-30 07:47:15.600346 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus

## 2026-05-30 07:47:15.856016 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis

## 2026-05-30 07:47:16.113401 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified

## 2026-05-30 07:47:16.393634 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified

## 2026-05-30 07:47:16.664024 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis

## 2026-05-30 07:47:16.921046 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis

## 2026-05-30 07:47:17.182631 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31

## 2026-05-30 07:47:17.445654 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae

## 2026-05-30 07:47:17.7224 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8

## 2026-05-30 07:47:17.995751 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae

## 2026-05-30 07:47:18.263647 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii

## 2026-05-30 07:47:18.531955 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii

## 2026-05-30 07:47:18.821445 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum

## 2026-05-30 07:47:19.084318 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA

## 2026-05-30 07:47:21.878293 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2026-05-30 07:47:21.880037 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified

## 2026-05-30 07:47:22.135902 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii

## 2026-05-30 07:47:22.41927 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae

## 2026-05-30 07:47:22.698663 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified

## 2026-05-30 07:47:22.983546 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis

## 2026-05-30 07:47:23.28317 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum

## 2026-05-30 07:47:23.592451 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus

## 2026-05-30 07:47:23.870735 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis

## 2026-05-30 07:47:24.161566 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii

## 2026-05-30 07:47:24.463485 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale

## 2026-05-30 07:47:24.762843 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis

## 2026-05-30 07:47:25.053409 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis

## 2026-05-30 07:47:25.702908 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-05-30 07:47:25.94597 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii

## 2026-05-30 07:47:26.190085 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens

## 2026-05-30 07:47:26.434205 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris

## 2026-05-30 07:47:26.678624 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii

## 2026-05-30 07:47:26.920264 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis

## 2026-05-30 07:47:27.161724 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum

## 2026-05-30 07:47:27.399879 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus

## 2026-05-30 07:47:27.648376 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii

## 2026-05-30 07:47:27.888265 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii

## 2026-05-30 07:47:28.1284 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae

## 2026-05-30 07:47:28.373801 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus

## 2026-05-30 07:47:28.621959 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum

## 2026-05-30 07:47:28.861072 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae

## 2026-05-30 07:47:29.106047 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae

## 2026-05-30 07:47:29.345843 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum

## 2026-05-30 07:47:29.583835 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis

## 2026-05-30 07:47:29.829495 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii

## 2026-05-30 07:47:30.134271 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques

## 2026-05-30 07:47:30.393534 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8

## 2026-05-30 07:47:30.663836 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum

## 2026-05-30 07:47:30.921489 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum

## 2026-05-30 07:47:31.195714 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis

## 2026-05-30 07:47:31.455705 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens

## 2026-05-30 07:47:31.714556 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi

## 2026-05-30 07:47:31.991347 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified

## 2026-05-30 07:47:32.256046 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens

## 2026-05-30 07:47:32.51916 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus

## 2026-05-30 07:47:32.782627 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae

## 2026-05-30 07:47:33.065507 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus

## 2026-05-30 07:47:33.326992 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris

## 2026-05-30 07:47:33.58849 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47

## 2026-05-30 07:47:36.281939 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2026-05-30 07:47:36.283523 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii

## 2026-05-30 07:47:36.539543 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale

## 2026-05-30 07:47:36.817454 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31

## 2026-05-30 07:47:37.102738 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis

## 2026-05-30 07:47:37.377388 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified

## 2026-05-30 07:47:37.652063 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-05-30 07:47:37.925548 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques

## 2026-05-30 07:47:38.202562 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum

## 2026-05-30 07:47:38.499049 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus

## 2026-05-30 07:47:38.767536 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli

## 2026-05-30 07:47:39.029943 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum

## 2026-05-30 07:47:39.312755 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified

## 2026-05-30 07:47:39.593063 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis

## 2026-05-30 07:47:39.911376 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens

## 2026-05-30 07:47:40.194383 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae

## 2026-05-30 07:47:40.503522 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii

## 2026-05-30 07:47:40.775372 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus

## 2026-05-30 07:47:41.048805 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified

## 2026-05-30 07:47:41.352289 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis

## 2026-05-30 07:47:41.631215 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii

## 2026-05-30 07:47:41.903073 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans

## 2026-05-30 07:47:42.208721 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii

## 2026-05-30 07:47:42.489215 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified

## 2026-05-30 07:47:42.787992 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii

## 2026-05-30 07:47:43.060464 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis

## 2026-05-30 07:47:43.354761 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri

## 2026-05-30 07:47:43.629959 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei

## 2026-05-30 07:47:43.92022 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis

## 2026-05-30 07:47:44.248986 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii

## 2026-05-30 07:47:47.090796 INFO::Plotting data for metadata number 4, antibiotics
## 2026-05-30 07:47:47.092618 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans

## 2026-05-30 07:47:47.35214 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis

## 2026-05-30 07:47:47.631747 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale

## 2026-05-30 07:47:47.922141 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus

## 2026-05-30 07:47:48.218257 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis

## 2026-05-30 07:47:48.490241 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena

## 2026-05-30 07:47:48.785381 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus

## 2026-05-30 07:47:49.061398 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii

## 2026-05-30 07:47:49.380775 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum

## 2026-05-30 07:47:49.681155 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae

## 2026-05-30 07:47:49.966518 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis

## 2026-05-30 07:47:50.245285 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii

## 2026-05-30 07:47:50.548091 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii

## 2026-05-30 07:47:50.832165 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified

## 2026-05-30 07:47:51.138436 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum

## 2026-05-30 07:47:51.424539 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-05-30 07:47:51.731486 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii

## 2026-05-30 07:47:52.018292 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31

## 2026-05-30 07:47:52.330336 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis

## 2026-05-30 07:47:52.611309 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii

## 2026-05-30 07:47:52.91091 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis

## 2026-05-30 07:47:53.217251 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens

## 2026-05-30 07:47:53.871408 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens

## 2026-05-30 07:47:54.18121 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron

## 2026-05-30 07:47:54.421831 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii

## 2026-05-30 07:47:54.651678 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae

## 2026-05-30 07:47:54.874467 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum

## 2026-05-30 07:47:55.106093 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques

## 2026-05-30 07:47:55.334027 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum

## 2026-05-30 07:47:55.571775 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis

## 2026-05-30 07:47:55.801281 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified

## 2026-05-30 07:47:56.031824 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar

## 2026-05-30 07:47:56.261817 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica

## 2026-05-30 07:47:56.487608 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8

## 2026-05-30 07:47:56.727711 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile

## 2026-05-30 07:47:56.957699 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47

## 2026-05-30 07:47:57.188167 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA

## 2026-05-30 07:47:57.423089 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila

## 2026-05-30 07:47:57.661896 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae

## 2026-05-30 07:47:57.891781 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus

## 2026-05-30 07:48:00.360153 INFO::Plotting data for metadata number 5, age
## 2026-05-30 07:48:00.361681 INFO::Creating scatter plot for continuous data, age vs Haemophilus.parainfluenzae

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

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

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

## 2026-05-30 07:48:00.66059 INFO::Creating scatter plot for continuous data, age vs Bifidobacterium.pseudocatenulatum

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

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

## 2026-05-30 07:48:00.959864 INFO::Creating scatter plot for continuous data, age vs Faecalibacterium.prausnitzii

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

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

## 2026-05-30 07:48:01.201685 INFO::Creating scatter plot for continuous data, age vs Clostridium.clostridioforme

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

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

## 2026-05-30 07:48:01.453485 INFO::Creating scatter plot for continuous data, age vs Veillonella.parvula

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

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

## 2026-05-30 07:48:01.684235 INFO::Creating scatter plot for continuous data, age vs Subdoligranulum.unclassified

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

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

## 2026-05-30 07:48:01.91849 INFO::Creating scatter plot for continuous data, age vs Clostridium.symbiosum

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

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

## 2026-05-30 07:48:02.162676 INFO::Creating scatter plot for continuous data, age vs Ruminococcus.gnavus

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

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

## 2026-05-30 07:48:02.416613 INFO::Creating scatter plot for continuous data, age vs Dialister.invisus

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

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

## 2026-05-30 07:48:02.653076 INFO::Creating scatter plot for continuous data, age vs Veillonella.dispar

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

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

## 2026-05-30 07:48:02.892197 INFO::Creating scatter plot for continuous data, age vs Veillonella.unclassified

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

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

## 2026-05-30 07:48:03.206685 INFO::Creating scatter plot for continuous data, age vs Bacteroides.thetaiotaomicron

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

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

## 2026-05-30 07:48:03.456333 INFO::Creating scatter plot for continuous data, age vs Ruminococcus.bromii

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

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

## 2026-05-30 07:48:03.700516 INFO::Creating scatter plot for continuous data, age vs Bacteroides.intestinalis

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

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

## 2026-05-30 07:48:03.93212 INFO::Creating scatter plot for continuous data, age vs Eubacterium.siraeum

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

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

## 2026-05-30 07:48:04.178686 INFO::Creating scatter plot for continuous data, age vs Prevotella.copri

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

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

## 2026-05-30 07:48:04.413332 INFO::Creating scatter plot for continuous data, age vs Alistipes.unclassified

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

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

## 2026-05-30 07:48:04.642313 INFO::Creating scatter plot for continuous data, age vs Bacteroidales.bacterium.ph8

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

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

## 2026-05-30 07:48:04.887016 INFO::Creating scatter plot for continuous data, age vs Bifidobacterium.longum

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

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

## 2026-05-30 07:48:05.118779 INFO::Creating scatter plot for continuous data, age vs Akkermansia.muciniphila

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

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

## 2026-05-30 07:48:05.374543 INFO::Creating scatter plot for continuous data, age vs Collinsella.aerofaciens

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

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

## 2026-05-30 07:48:05.605696 INFO::Creating scatter plot for continuous data, age vs Parabacteroides.distasonis

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

## 2026-05-30 07:48:08.197396 INFO::Plotting data for metadata number 6, diagnosis
## 2026-05-30 07:48:08.199129 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis

## 2026-05-30 07:48:08.471354 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila

## 2026-05-30 07:48:08.748834 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae

## 2026-05-30 07:48:09.039302 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis

## 2026-05-30 07:48:09.330383 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified

## 2026-05-30 07:48:09.606857 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme

## 2026-05-30 07:48:09.899582 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii

## 2026-05-30 07:48:10.176338 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii

## 2026-05-30 07:48:10.479688 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum

## 2026-05-30 07:48:10.76104 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum

## 2026-05-30 07:48:11.057241 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans

## 2026-05-30 07:48:11.392136 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii

## 2026-05-30 07:48:11.684596 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii

## 2026-05-30 07:48:11.994371 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii

## 2026-05-30 07:48:12.277665 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii

## 2026-05-30 07:48:12.580597 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified

## 2026-05-30 07:48:12.861239 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum

## 2026-05-30 07:48:13.158134 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis

## 2026-05-30 07:48:13.464576 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified

## 2026-05-30 07:48:13.762831 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii

## 2026-05-30 07:48:14.045627 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum

## 2026-05-30 07:48:14.347905 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis

## 2026-05-30 07:48:14.643916 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis

## 2026-05-30 07:48:14.946009 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila

## 2026-05-30 07:48:15.285751 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis

## 2026-05-30 07:48:15.584649 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified

## 2026-05-30 07:48:15.907941 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum

## 2026-05-30 07:48:16.211442 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii

## 2026-05-30 07:48:16.535406 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified

## 2026-05-30 07:48:16.852135 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris

## 2026-05-30 07:48:17.150403 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus

## 2026-05-30 07:48:17.470049 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus

## 2026-05-30 07:48:17.784202 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis

## 2026-05-30 07:48:18.105712 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale

## 2026-05-30 07:48:18.416838 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus

## 2026-05-30 07:48:18.733822 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis

## 2026-05-30 07:48:19.389906 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale

## 2026-05-30 07:48:19.633106 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii

## 2026-05-30 07:48:19.876918 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus

## 2026-05-30 07:48:20.112056 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii

## 2026-05-30 07:48:20.345701 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis

## 2026-05-30 07:48:20.585179 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae

## 2026-05-30 07:48:20.826063 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_1.27.0
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.6        biglm_0.9-3         xfun_0.57          
##  [4] bslib_0.11.0        ggplot2_4.0.3       lattice_0.22-9     
##  [7] numDeriv_2016.8-1.1 vctrs_0.7.3         tools_4.6.0        
## [10] Rdpack_2.6.6        generics_0.1.4      parallel_4.6.0     
## [13] tibble_3.3.1        DEoptimR_1.1-4      cluster_2.1.8.2    
## [16] pkgconfig_2.0.3     logging_0.10-111    pheatmap_1.0.13    
## [19] Matrix_1.7-5        data.table_1.18.4   RColorBrewer_1.1-3 
## [22] S7_0.2.2            lifecycle_1.0.5     compiler_4.6.0     
## [25] farver_2.1.2        lmerTest_3.2-1      permute_0.9-10     
## [28] htmltools_0.5.9     sys_3.4.3           buildtools_1.0.0   
## [31] sass_0.4.10         hash_2.2.6.4        yaml_2.3.12        
## [34] pillar_1.11.1       nloptr_2.2.1        crayon_1.5.3       
## [37] jquerylib_0.1.4     MASS_7.3-65         cachem_1.1.0       
## [40] vegan_2.7-5         reformulas_0.4.4    boot_1.3-32        
## [43] nlme_3.1-169        robustbase_0.99-7   tidyselect_1.2.1   
## [46] digest_0.6.39       mvtnorm_1.3-7       dplyr_1.2.1        
## [49] labeling_0.4.3      maketools_1.3.2     splines_4.6.0      
## [52] pcaPP_2.0-5         fastmap_1.2.0       grid_4.6.0         
## [55] cli_3.6.6           magrittr_2.0.5      withr_3.0.2        
## [58] scales_1.4.0        rmarkdown_2.31      lme4_2.0-1         
## [61] pbapply_1.7-4       evaluate_1.0.5      knitr_1.51         
## [64] rbibutils_2.4.1     mgcv_1.9-4          rlang_1.2.0        
## [67] Rcpp_1.1.1-1.1      glue_1.8.1          optparse_1.8.2     
## [70] DBI_1.3.0           minqa_1.2.8         jsonlite_2.0.0     
## [73] R6_2.6.1

Options

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Troubleshooting

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

- MaAsLin2 User Manual

Maaslin2