# Maaslin3 is running but is not able to generate any results

**URL:** <https://forum.biobakery.org/t/maaslin3-is-running-but-is-not-able-to-generate-any-results/8570>\
**Category:** MaAsLin\
**Created:** [October 21, 2025, 10:22am UTC](https://forum.biobakery.org/t/maaslin3-is-running-but-is-not-able-to-generate-any-results/8570 "2025-10-21T10:22:53Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Sayantan\_Bain](https://avatars.discourse-cdn.com/v4/letter/s/c5a1d2/32.png) [@Sayantan\_Bain](https://forum.biobakery.org/u/Sayantan_Bain)\
**Post date:** [October 21, 2025, 10:22am UTC](https://forum.biobakery.org/t/maaslin3-is-running-but-is-not-able-to-generate-any-results/8570/1 "2025-10-21T10:22:53Z")

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so this is my formula that im using:-

# Add reads column (total counts per sample)

metadata\_to\_test2$reads ← rowSums(abund\_matched)

fit\_out \<-maaslin3(  
input\_data = abund\_matched,  
input\_metadata = metadata\_to\_test2,  
output = “maaslin3\_output”,  
formula = ‘~ Age + Gender\_code + BMI + diabetes\_code + medHis\_highSugar\_code + antibiotics\_2weeks\_code + reads’,  
normalization = ‘TSS’,  
transform = ‘LOG’,  
augment = TRUE,  
standardize = TRUE,  
max\_significance = 0.1,  
median\_comparison\_abundance = TRUE,  
median\_comparison\_prevalence = FALSE,  
max\_pngs = 250,  
cores = 1  
)..and it is showing this for every amr gene family ethyltransferase (G1405)  
2025-10-21 15:20:15.749003 WARNING::Fitting problem for feature 1 returning NA  
2025-10-21 15:20:15.751084 INFO::Fitting model to feature number 2, 50S rRNA with mutation conferring resistance to macrolide antibiotics  
2025-10-21 15:20:15.753023 WARNING::Fitting problem for feature 2 returning NA  
|+ | 1 % ~01s 2025-10-21 15:20:15.754994 INFO::Fitting model to feature number 3, AAC(3)  
2025-10-21 15:20:15.757686 WARNING::Fitting problem for feature 3 returning NA  
2025-10-21 15:20:15.759442 INFO::Fitting model to feature number 4, AAC(6’)….and in the end I’m getting all zero values with nothing significant…where did i get wrong???

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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:** [October 21, 2025, 3:00pm UTC](https://forum.biobakery.org/t/maaslin3-is-running-but-is-not-able-to-generate-any-results/8570/2 "2025-10-21T15:00:14Z")

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Hi,

Nothing looks obviously wrong at first glance. Some things to start with:

1. What are the dimensions of your input data and how many total categories does that formula come out to?
2. Could you send 2-3 rows/columns of the anonymized input data? There might be something funky about the data that’s not obvious from just the MaAsLin 3 call

Will