# Error message Maaslin3

**URL:** <https://forum.biobakery.org/t/error-message-maaslin3/8152>\
**Category:** Downstream analysis and statistics\
**Created:** [June 18, 2025, 1:58am UTC](https://forum.biobakery.org/t/error-message-maaslin3/8152 "2025-06-18T01:58:04Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Katb](https://avatars.discourse-cdn.com/v4/letter/k/839c29/32.png) [@Katb](https://forum.biobakery.org/u/Katb)\
**Post date:** [June 18, 2025, 1:58am UTC](https://forum.biobakery.org/t/error-message-maaslin3/8152/1 "2025-06-18T01:58:04Z")

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Hello, I am trying to test for changes in prevalence of species at 2 time points. I have tried several iterations of the code and I keep getting the error message Error in maaslin\_fit(filtered\_data, transformed\_data, standardized\_metadata, :  
object ‘fit\_data\_abundance’ not found. It appears to be producing the feature tables and then goes through all of the model fitting, but then I get this error message. I don’t believe there is anything wrong with the format of my input data as I have tried running it in Maaslin2 and that works fine. The code I am using is below. Could you please assist with troubleshooting? Many thanks  
maaslin3(  
input\_data = taxa\_maaslin,  
input\_metadata = metadata\_filtered,  
output = ‘maaslin3\_time\_no\_confounders\_LOG\_refwk1\_11\_minprevTEST’, # output directory name  
min\_abundance = 0,  
min\_prevalence = 0.05,  
transform = ‘LOG’,  
warn\_prevalence = ‘FALSE’,  
normalization = ‘NONE’,  
evaluate\_only = ‘prevalence’,  
random\_effects = ‘PID’,  
fixed\_effects = c(‘Week’),  
reference = ‘1’, # Set reference level of Week to “1”  
correction = ‘BH’  
)

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**Author:** ![nearinj](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nearinj/32/2135_2.png) [@nearinj](https://forum.biobakery.org/u/nearinj)\
**Post date:** [June 18, 2025, 9:25pm UTC](https://forum.biobakery.org/t/error-message-maaslin3/8152/2 "2025-06-18T21:25:49Z")

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Hi @Katb ,

We are currently investigating what’s going on here.

In the mean time while we look at this you should adjust your parameters for:

`warn_prevalence=FALSE`  
(no quotes around FALSE)

and

`reference="Week,1"`

Thanks,  
Jacob Nearing

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**Author:** ![WillNickols](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/willnickols/32/3223_2.png) [@WillNickols](https://forum.biobakery.org/u/WillNickols)\
**Post date:** [June 18, 2025, 9:46pm UTC](https://forum.biobakery.org/t/error-message-maaslin3/8152/3 "2025-06-18T21:46:52Z")

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Hi @Katb,

That was a bug on our end - if you re-install with:

```auto
devtools::install_github('https://github.com/biobakery/maaslin3', ref = 'devel')

```

it should work now. Let me know if it’s still having issues!

Also, `warn_prevalence=FALSE` shouldn’t have quotes on `FALSE`.

Will

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**Author:** ![Katb](https://avatars.discourse-cdn.com/v4/letter/k/839c29/32.png) [@Katb](https://forum.biobakery.org/u/Katb)\
**Post date:** [June 18, 2025, 11:37pm UTC](https://forum.biobakery.org/t/error-message-maaslin3/8152/4 "2025-06-18T23:37:17Z")

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Thank you so much for your help.