# Error running MaAsLin3 for genus level data only

**URL:** <https://forum.biobakery.org/t/error-running-maaslin3-for-genus-level-data-only/8941>\
**Category:** Downstream analysis and statistics\
**Created:** [June 3, 2026, 6:41pm UTC](https://forum.biobakery.org/t/error-running-maaslin3-for-genus-level-data-only/8941 "2026-06-03T18:41:49Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![sfontaine](https://avatars.discourse-cdn.com/v4/letter/s/35a633/32.png) [@sfontaine](https://forum.biobakery.org/u/sfontaine)\
**Post date:** [June 3, 2026, 6:41pm UTC](https://forum.biobakery.org/t/error-running-maaslin3-for-genus-level-data-only/8941/1 "2026-06-03T18:41:49Z")

</div>

Hi there!

I am having an error running MaAsLin3 in R only for genus level data. I have run the exact same code with the same metadata with family and phylum level counts and have not had any issue.

```auto
Error in `[.data.frame`(new_normalized_data, rownames(transformed_data), : 
  undefined columns selected

```

I have double checked that the row names in the metadata and genus taxa data match exactly, and have removed any special characters from the genus names.

Code I’m trying to run:

```auto
genus_out <- maaslin3(input_data = gen_table,
                       input_metadata = metadata_mixed3,
                       output = '~/QIIME2/Xenopus/Maaslin_mixed3_genus_output.txt',
                       formula = 'group(Species) + reads_cleaned + (1|Tank)',
                       normalization = 'TSS',
                       transform = 'LOG',
                       augment = TRUE,
                       standardize = TRUE,
                       max_significance = 0.05,
                       min_prevalence = 0.05,
                       median_comparison_abundance = TRUE,
                       median_comparison_prevalence = FALSE,
                       max_pngs = 10,
                       cores = 1)

```

Similar code for family level that runs perfectly

```auto
family_out <- maaslin3(input_data = fam_table,
                      input_metadata = metadata_mixed3,
                      output = '~/QIIME2/Xenopus/Maaslin_mixed3_family_output.txt',
                      formula = 'group(Species) + reads_cleaned + (1|Tank)',
                      normalization = 'TSS',
                      transform = 'LOG',
                      augment = TRUE,
                      standardize = TRUE,
                      max_significance = 0.05,
                      min_prevalence = 0.05,
                      median_comparison_abundance = TRUE,
                      median_comparison_prevalence = FALSE,
                      max_pngs = 10,
                      cores = 1)

```

Header of the data I’m trying to run

```auto
head(metadata_mixed3)
          Tank Species_Treatment Treatment Mass Body.Length Development Species overall_treatment detailed_treatment SampleID reads_cleaned
IST113 XLXBXT1 XL_Mixed_3 Mixed_3 0.092 9.60 53 XL Mixed Mixed_3 IST113 47066
IST114 XLXBXT1 XT_Mixed_3 Mixed_3 0.046 7.43 48 XT Mixed Mixed_3 IST114 22594
IST116 XLXBXT1 XT_Mixed_3 Mixed_3 0.041 7.08 48 XT Mixed Mixed_3 IST116 32423
IST117 XLXBXT1 XB_Mixed_3 Mixed_3 0.039 7.59 49 XB Mixed Mixed_3 IST117 31246
IST118 XLXBXT1 XB_Mixed_3 Mixed_3 0.041 8.24 49 XB Mixed Mixed_3 IST118 38745
IST139 XLXBXT2 XL_Mixed_3 Mixed_3 0.110 9.84 53 XL Mixed Mixed_3 IST139 14768

```

```auto
> head(gen_table)
       Pseudoxanthobacter 67_14 WPS_2 Bacteroides Chitinivorax Parabacteroides Anaerovorax Acholeplasma Butyricimonas Anaerococcus Erysipelatoclostridium
IST113 0 0 0 7279 0 2701 89 51 0 0 0
IST114 0 0 0 3715 0 0 41 0 0 0 0
IST116 0 0 0 6752 0 0 116 0 0 0 0
IST117 0 0 0 1306 0 899 56 0 0 0 0
IST118 0 0 0 5999 0 438 40 0 0 0 0
IST139 0 0 0 2561 0 1265 65 0 10 0 0

```

Thanks so much in advance!

---

<div class="post-metadata">

**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 3, 2026, 7:11pm UTC](https://forum.biobakery.org/t/error-running-maaslin3-for-genus-level-data-only/8941/2 "2026-06-03T19:11:57Z")

</div>

Hi,

Nothing seems obviously wrong in the data you posted. Would you be able to send small chunks of the metadata, the family/phylum table that works, and the genus table that doesn’t (willnickols@g.harvard.edu) so I can debug it on my side and figure out what’s wrong? That’ll probably be faster than guessing things over the forum.

In the meantime, is there a reason you’re using the `group()` strategy in the formula? We haven’t found many cases where this is actually preferable over just including the variable directly, and there might be some edge case with `group()` that’s causing issues.

Will