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"
## 2026-10-10 13:47:15.979079 INFO::Writing function arguments to log file
## 2026-10-10 13:47:16.06598 INFO::Verifying options selected are valid
## 2026-10-10 13:47:16.088504 INFO::Determining format of input files
## 2026-10-10 13:47:16.089524 INFO::Input format is data samples as rows and metadata samples as rows
## 2026-10-10 13:47:16.093207 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2026-10-10 13:47:16.094097 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2026-10-10 13:47:16.095857 INFO::Filter data based on min abundance and min prevalence
## 2026-10-10 13:47:16.096438 INFO::Total samples in data: 1595
## 2026-10-10 13:47:16.096972 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2026-10-10 13:47:16.1008 INFO::Total filtered features: 0
## 2026-10-10 13:47:16.101505 INFO::Filtered feature names from abundance and prevalence filtering:
## 2026-10-10 13:47:16.108338 INFO::Total filtered features with variance filtering: 0
## 2026-10-10 13:47:16.109175 INFO::Filtered feature names from variance filtering:
## 2026-10-10 13:47:16.109769 INFO::Running selected normalization method: TSS
## 2026-10-10 13:47:16.907564 INFO::Bypass z-score application to metadata
## 2026-10-10 13:47:16.90845 INFO::Running selected transform method: LOG
## 2026-10-10 13:47:16.930816 INFO::Running selected analysis method: LM
## 2026-10-10 13:47:17.162736 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis

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

## 2026-10-10 13:47:17.558352 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2026-10-10 13:47:17.659742 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2026-10-10 13:47:17.810235 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum

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

## 2026-10-10 13:47:17.900527 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2026-10-10 13:47:18.009048 INFO::Fitting model to feature number 6, Bacteroides.caccae

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

## 2026-10-10 13:47:18.101146 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2026-10-10 13:47:18.196272 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2026-10-10 13:47:18.296431 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2026-10-10 13:47:18.39416 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2026-10-10 13:47:18.492254 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

## 2026-10-10 13:47:18.574186 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

## 2026-10-10 13:47:18.673239 INFO::Fitting model to feature number 12, Bacteroides.fragilis

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

## 2026-10-10 13:47:18.765064 INFO::Fitting model to feature number 13, Bacteroides.intestinalis

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

## 2026-10-10 13:47:18.864511 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2026-10-10 13:47:18.958343 INFO::Fitting model to feature number 15, Bacteroides.ovatus

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

## 2026-10-10 13:47:19.052884 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2026-10-10 13:47:19.155175 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2026-10-10 13:47:19.257926 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron

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

## 2026-10-10 13:47:19.350374 INFO::Fitting model to feature number 19, Bacteroides.uniformis

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

## 2026-10-10 13:47:19.447623 INFO::Fitting model to feature number 20, Bacteroides.vulgatus

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

## 2026-10-10 13:47:19.551203 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens

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

## 2026-10-10 13:47:19.642194 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2026-10-10 13:47:19.743428 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2026-10-10 13:47:19.839948 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2026-10-10 13:47:19.944974 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2026-10-10 13:47:20.039464 INFO::Fitting model to feature number 26, Parabacteroides.distasonis

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

## 2026-10-10 13:47:20.136698 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2026-10-10 13:47:20.239602 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2026-10-10 13:47:20.336232 INFO::Fitting model to feature number 29, Parabacteroides.unclassified

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

## 2026-10-10 13:47:20.433681 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2026-10-10 13:47:20.53134 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2026-10-10 13:47:20.633032 INFO::Fitting model to feature number 32, Prevotella.copri

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

## 2026-10-10 13:47:20.731531 INFO::Fitting model to feature number 33, Alistipes.finegoldii

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

## 2026-10-10 13:47:20.82742 INFO::Fitting model to feature number 34, Alistipes.onderdonkii

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

## 2026-10-10 13:47:20.921896 INFO::Fitting model to feature number 35, Alistipes.putredinis

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

## 2026-10-10 13:47:21.205472 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2026-10-10 13:47:21.301805 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2026-10-10 13:47:21.399212 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2026-10-10 13:47:21.50866 INFO::Fitting model to feature number 39, Clostridium.bolteae

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

## 2026-10-10 13:47:21.60618 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

## 2026-10-10 13:47:21.680527 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

## 2026-10-10 13:47:21.776404 INFO::Fitting model to feature number 41, Clostridium.clostridioforme

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

## 2026-10-10 13:47:21.8633 INFO::Fitting model to feature number 42, Clostridium.hathewayi

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

## 2026-10-10 13:47:21.952212 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2026-10-10 13:47:22.063969 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2026-10-10 13:47:22.156746 INFO::Fitting model to feature number 45, Clostridium.symbiosum

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

## 2026-10-10 13:47:22.24769 INFO::Fitting model to feature number 46, Flavonifractor.plautii

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

## 2026-10-10 13:47:22.350636 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2026-10-10 13:47:22.444725 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2026-10-10 13:47:22.542926 INFO::Fitting model to feature number 49, Eubacterium.rectale

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

## 2026-10-10 13:47:22.638722 INFO::Fitting model to feature number 50, Eubacterium.siraeum

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

## 2026-10-10 13:47:22.738784 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31

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

## 2026-10-10 13:47:22.831109 INFO::Fitting model to feature number 52, Eubacterium.ventriosum

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

## 2026-10-10 13:47:22.918998 INFO::Fitting model to feature number 53, Ruminococcus.gnavus

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

## 2026-10-10 13:47:23.017279 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2026-10-10 13:47:23.109648 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2026-10-10 13:47:23.203148 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2026-10-10 13:47:23.305365 INFO::Fitting model to feature number 57, Dorea.longicatena

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

## 2026-10-10 13:47:23.397612 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA

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

## 2026-10-10 13:47:23.492847 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA

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

## 2026-10-10 13:47:23.589106 INFO::Fitting model to feature number 60, Roseburia.hominis

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

## 2026-10-10 13:47:23.682776 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2026-10-10 13:47:23.780029 INFO::Fitting model to feature number 62, Roseburia.inulinivorans

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

## 2026-10-10 13:47:23.87009 INFO::Fitting model to feature number 63, Roseburia.unclassified

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

## 2026-10-10 13:47:23.960725 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2026-10-10 13:47:24.066571 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2026-10-10 13:47:24.159306 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2026-10-10 13:47:24.255057 INFO::Fitting model to feature number 67, Ruminococcus.bromii

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

## 2026-10-10 13:47:24.347252 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2026-10-10 13:47:24.438437 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2026-10-10 13:47:24.542146 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified

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

## 2026-10-10 13:47:24.633925 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2026-10-10 13:47:24.725415 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2026-10-10 13:47:24.826639 INFO::Fitting model to feature number 73, Dialister.invisus

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

## 2026-10-10 13:47:24.915265 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2026-10-10 13:47:25.017077 INFO::Fitting model to feature number 75, Veillonella.dispar

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

## 2026-10-10 13:47:25.108965 INFO::Fitting model to feature number 76, Veillonella.parvula

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

## 2026-10-10 13:47:25.203488 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2026-10-10 13:47:25.295164 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2026-10-10 13:47:25.397505 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2026-10-10 13:47:25.490164 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2026-10-10 13:47:25.591799 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2026-10-10 13:47:25.691781 INFO::Fitting model to feature number 82, Escherichia.coli
## 2026-10-10 13:47:25.793888 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2026-10-10 13:47:25.882283 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae

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

## 2026-10-10 13:47:25.977636 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae

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

## 2026-10-10 13:47:26.070612 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2026-10-10 13:47:26.1728 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2026-10-10 13:47:26.488861 INFO::Counting total values for each feature
## 2026-10-10 13:47:26.510722 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2026-10-10 13:47:26.571631 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2026-10-10 13:47:26.632479 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2026-10-10 13:47:26.720621 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2026-10-10 13:47:26.75966 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2026-10-10 13:47:26.781941 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2026-10-10 13:47:26.785657 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2026-10-10 13:47:26.788913 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
## 2026-10-10 13:47:26.790528 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2026-10-10 13:47:27.196898 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2026-10-10 13:47:27.201004 INFO::Plotting associations from most to least significant, grouped by metadata
## 2026-10-10 13:47:27.201652 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2026-10-10 13:47:27.202783 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii

## 2026-10-10 13:47:27.549064 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified

## 2026-10-10 13:47:27.821911 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis

## 2026-10-10 13:47:28.081696 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale

## 2026-10-10 13:47:28.371619 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus

## 2026-10-10 13:47:28.632293 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus

## 2026-10-10 13:47:28.890178 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum

## 2026-10-10 13:47:29.150723 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified

## 2026-10-10 13:47:29.411269 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans

## 2026-10-10 13:47:29.679395 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis

## 2026-10-10 13:47:29.943507 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron

## 2026-10-10 13:47:30.2058 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis

## 2026-10-10 13:47:30.469406 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis

## 2026-10-10 13:47:30.728473 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei

## 2026-10-10 13:47:30.989123 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii

## 2026-10-10 13:47:31.249898 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens

## 2026-10-10 13:47:31.515832 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum

## 2026-10-10 13:47:31.781828 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena

## 2026-10-10 13:47:32.044159 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae

## 2026-10-10 13:47:32.308151 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-10-10 13:47:32.57657 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli

## 2026-10-10 13:47:32.837821 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae

## 2026-10-10 13:47:33.140774 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified

## 2026-10-10 13:47:33.403396 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii

## 2026-10-10 13:47:33.673735 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens

## 2026-10-10 13:47:33.944305 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris

## 2026-10-10 13:47:34.224402 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes

## 2026-10-10 13:47:34.499115 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis

## 2026-10-10 13:47:34.770507 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii

## 2026-10-10 13:47:35.0398 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii

## 2026-10-10 13:47:35.302197 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis

## 2026-10-10 13:47:35.572931 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara

## 2026-10-10 13:47:35.842069 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum

## 2026-10-10 13:47:36.103335 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae

## 2026-10-10 13:47:36.3686 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified

## 2026-10-10 13:47:36.64801 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens

## 2026-10-10 13:47:36.913855 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus

## 2026-10-10 13:47:37.184371 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme

## 2026-10-10 13:47:37.463216 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii

## 2026-10-10 13:47:37.752754 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii

## 2026-10-10 13:47:38.013938 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum

## 2026-10-10 13:47:38.279387 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris

## 2026-10-10 13:47:38.539758 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47

## 2026-10-10 13:47:38.804855 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus

## 2026-10-10 13:47:39.074636 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii

## 2026-10-10 13:47:39.338973 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis

## 2026-10-10 13:47:39.59808 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified

## 2026-10-10 13:47:39.861671 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques

## 2026-10-10 13:47:40.124157 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified

## 2026-10-10 13:47:40.399584 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus

## 2026-10-10 13:47:40.663205 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis

## 2026-10-10 13:47:40.927053 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified

## 2026-10-10 13:47:41.206802 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified

## 2026-10-10 13:47:41.467211 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis

## 2026-10-10 13:47:41.720228 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis

## 2026-10-10 13:47:41.98954 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31

## 2026-10-10 13:47:42.280917 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae

## 2026-10-10 13:47:42.545363 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8

## 2026-10-10 13:47:42.811603 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae

## 2026-10-10 13:47:43.082167 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii

## 2026-10-10 13:47:43.362826 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii

## 2026-10-10 13:47:43.652349 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum

## 2026-10-10 13:47:43.928355 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA

## 2026-10-10 13:47:46.752075 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2026-10-10 13:47:46.75362 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified

## 2026-10-10 13:47:47.008738 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii

## 2026-10-10 13:47:47.29156 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae

## 2026-10-10 13:47:47.820537 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified

## 2026-10-10 13:47:48.071979 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis

## 2026-10-10 13:47:48.324917 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum

## 2026-10-10 13:47:48.57592 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus

## 2026-10-10 13:47:48.819894 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis

## 2026-10-10 13:47:49.072019 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii

## 2026-10-10 13:47:49.319112 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale

## 2026-10-10 13:47:49.565048 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis

## 2026-10-10 13:47:49.815736 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis

## 2026-10-10 13:47:50.063601 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-10-10 13:47:50.311706 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii

## 2026-10-10 13:47:50.565704 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens

## 2026-10-10 13:47:50.822215 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris

## 2026-10-10 13:47:51.079691 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii

## 2026-10-10 13:47:51.335526 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis

## 2026-10-10 13:47:51.586755 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum

## 2026-10-10 13:47:51.838595 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus

## 2026-10-10 13:47:52.087188 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii

## 2026-10-10 13:47:52.338295 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii

## 2026-10-10 13:47:52.625685 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae

## 2026-10-10 13:47:52.886891 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus

## 2026-10-10 13:47:53.184217 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum

## 2026-10-10 13:47:53.449471 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae

## 2026-10-10 13:47:53.70887 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae

## 2026-10-10 13:47:53.961851 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum

## 2026-10-10 13:47:54.2161 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis

## 2026-10-10 13:47:54.472407 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii

## 2026-10-10 13:47:54.737272 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques

## 2026-10-10 13:47:54.992781 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8

## 2026-10-10 13:47:55.257901 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum

## 2026-10-10 13:47:55.511495 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum

## 2026-10-10 13:47:55.784575 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis

## 2026-10-10 13:47:56.037472 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens

## 2026-10-10 13:47:56.291575 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi

## 2026-10-10 13:47:56.559799 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified

## 2026-10-10 13:47:56.822219 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens

## 2026-10-10 13:47:57.117874 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus

## 2026-10-10 13:47:57.385736 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae

## 2026-10-10 13:47:57.653734 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus

## 2026-10-10 13:47:57.932693 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris

## 2026-10-10 13:47:58.201098 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47

## 2026-10-10 13:48:00.881466 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2026-10-10 13:48:00.882961 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii

## 2026-10-10 13:48:01.137108 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale

## 2026-10-10 13:48:01.421479 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31

## 2026-10-10 13:48:01.698355 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis

## 2026-10-10 13:48:01.965808 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified

## 2026-10-10 13:48:02.276811 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-10-10 13:48:02.559325 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques

## 2026-10-10 13:48:02.835471 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum

## 2026-10-10 13:48:03.113492 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus

## 2026-10-10 13:48:03.389092 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli

## 2026-10-10 13:48:03.681385 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum

## 2026-10-10 13:48:03.96898 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified

## 2026-10-10 13:48:04.254432 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis

## 2026-10-10 13:48:04.528886 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens

## 2026-10-10 13:48:04.821894 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae

## 2026-10-10 13:48:05.100097 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii

## 2026-10-10 13:48:05.365304 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus

## 2026-10-10 13:48:05.648941 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified

## 2026-10-10 13:48:05.926196 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis

## 2026-10-10 13:48:06.203705 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii

## 2026-10-10 13:48:06.485764 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans

## 2026-10-10 13:48:06.802348 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii

## 2026-10-10 13:48:07.09666 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified

## 2026-10-10 13:48:07.377111 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii

## 2026-10-10 13:48:07.652638 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis

## 2026-10-10 13:48:07.943152 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri

## 2026-10-10 13:48:08.242172 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei

## 2026-10-10 13:48:08.516616 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis

## 2026-10-10 13:48:08.808539 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii

## 2026-10-10 13:48:11.640291 INFO::Plotting data for metadata number 4, antibiotics
## 2026-10-10 13:48:11.641933 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans

## 2026-10-10 13:48:11.938875 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis

## 2026-10-10 13:48:12.246596 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale

## 2026-10-10 13:48:12.553437 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus

## 2026-10-10 13:48:12.852348 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis

## 2026-10-10 13:48:13.128046 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena

## 2026-10-10 13:48:13.439725 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus

## 2026-10-10 13:48:13.738084 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii

## 2026-10-10 13:48:14.012424 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum

## 2026-10-10 13:48:14.295069 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae

## 2026-10-10 13:48:14.585099 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis

## 2026-10-10 13:48:14.852199 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii

## 2026-10-10 13:48:15.146385 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii

## 2026-10-10 13:48:15.423386 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified

## 2026-10-10 13:48:15.721123 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum

## 2026-10-10 13:48:15.993321 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA

## 2026-10-10 13:48:16.55618 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii

## 2026-10-10 13:48:16.80091 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31

## 2026-10-10 13:48:17.037412 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis

## 2026-10-10 13:48:17.273301 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii

## 2026-10-10 13:48:17.513694 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis

## 2026-10-10 13:48:17.756539 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens

## 2026-10-10 13:48:17.992626 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens

## 2026-10-10 13:48:18.234499 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron

## 2026-10-10 13:48:18.474687 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii

## 2026-10-10 13:48:18.722478 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae

## 2026-10-10 13:48:18.960575 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum

## 2026-10-10 13:48:19.204849 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques

## 2026-10-10 13:48:19.444841 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum

## 2026-10-10 13:48:19.694102 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis

## 2026-10-10 13:48:19.939989 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified

## 2026-10-10 13:48:20.183643 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar

## 2026-10-10 13:48:20.424524 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica

## 2026-10-10 13:48:20.669757 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8

## 2026-10-10 13:48:20.939136 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile

## 2026-10-10 13:48:21.19418 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47

## 2026-10-10 13:48:21.446328 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA

## 2026-10-10 13:48:21.701814 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila

## 2026-10-10 13:48:21.953147 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae

## 2026-10-10 13:48:22.208227 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus

## 2026-10-10 13:48:24.773269 INFO::Plotting data for metadata number 5, age
## 2026-10-10 13:48:24.774757 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()`).

## 2026-10-10 13:48:25.082719 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()`).

## 2026-10-10 13:48:25.411988 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()`).

## 2026-10-10 13:48:25.649379 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()`).

## 2026-10-10 13:48:25.897768 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()`).

## 2026-10-10 13:48:26.177446 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()`).

## 2026-10-10 13:48:26.438621 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()`).

## 2026-10-10 13:48:26.692849 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()`).

## 2026-10-10 13:48:26.936307 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()`).

## 2026-10-10 13:48:27.185045 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()`).

## 2026-10-10 13:48:27.430618 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()`).

## 2026-10-10 13:48:27.682768 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()`).

## 2026-10-10 13:48:27.924207 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()`).

## 2026-10-10 13:48:28.168307 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()`).

## 2026-10-10 13:48:28.418488 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()`).

## 2026-10-10 13:48:28.65307 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()`).

## 2026-10-10 13:48:28.889151 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()`).

## 2026-10-10 13:48:29.145146 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()`).

## 2026-10-10 13:48:29.377815 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()`).

## 2026-10-10 13:48:29.627405 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()`).

## 2026-10-10 13:48:29.868975 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()`).

## 2026-10-10 13:48:30.155502 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()`).

## 2026-10-10 13:48:32.767031 INFO::Plotting data for metadata number 6, diagnosis
## 2026-10-10 13:48:32.768452 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis

## 2026-10-10 13:48:33.034457 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila

## 2026-10-10 13:48:33.322336 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae

## 2026-10-10 13:48:33.598703 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis

## 2026-10-10 13:48:33.894763 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified

## 2026-10-10 13:48:34.191747 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme

## 2026-10-10 13:48:34.483269 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii

## 2026-10-10 13:48:34.787692 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii

## 2026-10-10 13:48:35.086839 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum

## 2026-10-10 13:48:35.365134 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum

## 2026-10-10 13:48:35.662414 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans

## 2026-10-10 13:48:35.940735 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii

## 2026-10-10 13:48:36.240277 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii

## 2026-10-10 13:48:36.51532 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii

## 2026-10-10 13:48:36.810221 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii

## 2026-10-10 13:48:37.097684 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified

## 2026-10-10 13:48:37.376193 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum

## 2026-10-10 13:48:37.67487 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis

## 2026-10-10 13:48:37.968351 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified

## 2026-10-10 13:48:38.253322 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii

## 2026-10-10 13:48:38.563905 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum

## 2026-10-10 13:48:38.868023 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis

## 2026-10-10 13:48:39.152685 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis

## 2026-10-10 13:48:39.458574 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila

## 2026-10-10 13:48:39.748533 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis

## 2026-10-10 13:48:40.043755 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified

## 2026-10-10 13:48:40.350487 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum

## 2026-10-10 13:48:40.665823 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii

## 2026-10-10 13:48:40.962503 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified

## 2026-10-10 13:48:41.265034 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris

## 2026-10-10 13:48:41.566067 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus

## 2026-10-10 13:48:41.865102 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus

## 2026-10-10 13:48:42.438735 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis

## 2026-10-10 13:48:42.695815 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale

## 2026-10-10 13:48:42.948559 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus

## 2026-10-10 13:48:43.201307 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis

## 2026-10-10 13:48:43.448833 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale

## 2026-10-10 13:48:43.701237 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii

## 2026-10-10 13:48:43.956439 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus

## 2026-10-10 13:48:44.201207 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii

## 2026-10-10 13:48:44.451179 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis

## 2026-10-10 13:48:44.708671 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae

## 2026-10-10 13:48:44.966775 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 26.04.1 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_0.61          
##  [4] bslib_0.12.0        ggplot2_4.0.3       lattice_0.23-1     
##  [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_1.2-2      cluster_2.1.8.3    
## [16] pkgconfig_2.0.3     logging_0.10-111    pheatmap_1.0.13    
## [19] Matrix_1.7-6        data.table_1.18.6.1 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_7.3-66         cachem_1.1.0       
## [40] vegan_2.7-6         reformulas_0.4.4    boot_1.3-32        
## [43] nlme_3.1-171        robustbase_0.99-7   tidyselect_1.2.1   
## [46] digest_0.6.39       mvtnorm_1.4-2       dplyr_1.2.1        
## [49] labeling_0.4.3      maketools_1.3.2     splines_4.6.1      
## [52] pcaPP_2.0-7         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_2.32      otel_0.2.0         
## [61] lme4_2.0-6          pbapply_1.7-5       evaluate_1.0.5     
## [64] knitr_1.52          rbibutils_2.4.1     mgcv_1.9-4         
## [67] rlang_1.3.0         Rcpp_1.1.2          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