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.