R Session aborts when running Maaslin2

Hello! I have been trying to use Maaslin2 (Version ‘1.16.0’) with different subset of my 16S data. When I try to run the following command (with any of my data example input and metadata attached) it aborts my R session:

Code:
Maaslin ← Maaslin2(input_data = InputFeces16, input_metadata = InputMetadata, “pilot_maaslin2_output”,
fixed_effects = c(“Treatment”, “DietBox”, “Gender”),
random_effects = c(“Mouse”,“Parents”, “Cage”),
reference = c(“Treatment,Control”))

Error before R crashes:
[1] “Warning: Deleting existing log file: pilot_maaslin2_output/maaslin2.log”
2024-10-19 21:32:24.783026 INFO::Writing function arguments to log file
2024-10-19 21:32:24.79628 INFO::Verifying options selected are valid
2024-10-19 21:32:24.824881 INFO::Determining format of input files
2024-10-19 21:32:24.911929 INFO::Input format is data samples as rows and metadata samples as rows
2024-10-19 21:32:25.128515 INFO::Formula for random effects: expr ~ (1 | Mouse) + (1 | Parents) + (1 | Cage)
2024-10-19 21:32:25.129796 INFO::Formula for fixed effects: expr ~ Treatment + DietBox + Gender
2024-10-19 21:32:25.133112 INFO::Filter data based on min abundance and min prevalence
2024-10-19 21:32:25.133824 INFO::Total samples in data: 32435
2024-10-19 21:32:25.134278 INFO::Min samples required with min abundance for a feature not to be filtered: 3243.500000
2024-10-19 21:32:25.151582 INFO::Total filtered features: 0
2024-10-19 21:32:25.152788 INFO::Filtered feature names from abundance and prevalence filtering:
Warning: NAs introduced by coercionWarning: NAs introduced by coercionWarning: NAs introduced by coercionWarning: NAs introduced by coercionWarning: NAs introduced by coercionWarning: NAs introduced by coercionWarning: NAs introduced by coercion2024-10-19 21:32:25.193874 INFO::Total filtered features with variance filtering: 8
2024-10-19 21:32:25.194685 INFO::Filtered feature names from variance filtering: Sample, SampleType, OTU, Kingdom, Phylum, Class, Order, Age.weeks.
2024-10-19 21:32:25.195193 INFO::Running selected normalization method: TSS
2024-10-19 21:32:25.249992 INFO::Applying z-score to standardize continuous metadata
2024-10-19 21:32:25.255631 INFO::Running selected transform method: LOG
2024-10-19 21:32:25.268095 INFO::Running selected analysis method: LM
| | 0 % ~calculating 2024-10-19 21:32:25.276529 INFO::Fitting model to feature number 1, X.2

InputFeces16.tsv (3.7 MB)
InputFeces16Meta.tsv (7.0 MB)

Thank you for your help! I am not sure why this is happening or how to troubleshoot it.

Hi @mjs ,

It looks like your feature data is in long format. MaAsLin2 expects the data is be in “wide” format meaning the rows should be taxa and the columns should be samples (with the abundances in each data cell).

Can you try reformatting your data and running it again.

Thanks,
Jacob Nearing