# Class is missing from the lefse output

**URL:** <https://forum.mothur.org/t/class-is-missing-from-the-lefse-output/22380>\
**Category:** mothur bugs\
**Created:** [October 21, 2025, 4:34pm UTC](https://forum.mothur.org/t/class-is-missing-from-the-lefse-output/22380 "2025-10-21T16:34:08Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![vherve](https://avatars.discourse-cdn.com/v4/letter/v/b5e925/32.png) [@vherve](https://forum.mothur.org/u/vherve)\
**Post date:** [October 21, 2025, 4:34pm UTC](https://forum.mothur.org/t/class-is-missing-from-the-lefse-output/22380/1 "2025-10-21T16:34:08Z")

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Dear mothur team,

I am currently using mothur 1.48.0 (and 1.48.3 too, but the issue below remains the same) with Ubuntu 24.04.

I do have a problem with the Lefse analysis, more specifically with the output. A few years ago, with older version of mothur and ubuntu, in the Lefse output there were 5 columns:

OTU LogMaxMean Class LDA pValue

Now in the output, I only have 4 columns with “Class” being missing:

OTU logMaxMean LDA pValue

So as you can imagine, it is a bit annoying because I can identify discriminant OTU but I can not know directly from the output, in which class/ecosystem this OTU is more abundant.

I am running this command :

lefse(shared=data16S.shared, design=data16S.design, lda=3, iters=1000)

and here is the data16S.design file

| group | treatment | |
| --- | --- | --- |
| PAP0001 | Marine | |
| PAP0003 | Marine | |
| PAP0004 | Marine | |
| PAP0005 | Marine | |
| PAP0006 | Marine | |
| PAP0007 | Marine | |
| PAP0008 | Marine | |
| PAP0009 | Marine | |
| PAP0010 | Marine | |
| PAP0011 | Marine | |
| PAP0012 | Marine | |
| PAP0013 | Marine | |
| PAP0014 | Marine | |
| PAP0015 | Mangrove | |
| PAP0016 | Mangrove | |
| PAP0017 | Mangrove | |
| PAP0018 | Mangrove | |
| PAP0019 | Mangrove | |
| PAP0020 | Marine | |
| PAP0021 | Marine | |
| PAP0022 | Marine | |
| PAP0023 | Marine | |
| PAP0024 | Marine | |
| PAP0025 | Urban | |
| PAP0026 | Urban | |
| PAP0027 | Urban | |
| PAP0028 | Mangrove | |
| PAP0029 | Urban | |
| PAP0030 | Urban | |
| PAP0031 | Marine | |
| PAP0032 | Urban | |
| PAP0033 | Urban | |
| PAP0034 | Urban | |
| PAP0035 | Urban | |
| PAP0036 | Urban | |
| PAP0037 | Urban | |
| PAP0038 | Urban | |
| PAP0039 | Urban | |
| PAP0040 | Mangrove | |
| PAP0041 | Urban | |
| PAP0044 | Urban | |
| PAP0045 | Urban | |
| PAP0046 | Urban | |
| PAP0047 | Urban | |
| PAP0048 | Urban | |
| PAP0049 | Urban | |
| PAP0051 | Urban | |
| PAP0052 | Urban | |
| PAP0053 | Urban | |
| PAP0054 | Urban | |
| PAP0055 | Urban | |
| PAP0056 | Marine | |
| PAP0057 | Marine | |
| PAP0058 | Marine | |
| PAP0059 | Marine | |
| PAP0060 | Marine | |
| PAP0061 | Marine | |
| PAP0062 | Marine | |
| PAP0063 | Marine | |
| PAP0064 | Marine | |
| PAP0065 | Marine | |
| PAP0067 | Marine | |
| PAP0068 | Marine | |
| PAP0069 | Marine | |
| PAP0070 | Marine | |
| PAP0071 | Marine | |
| PAP0072 | Marine | |
| PAP0073 | Marine | |
| PAP0074 | Marine | |
| PAP0075 | Marine | |
| PAP0076 | Marine | |
| PAP0077 | Marine | |
| PAP0078 | Marine | |
| PAP0079 | Marine | |
| PAP0080 | Marine | |
| PAP0081 | Marine | |
| PAP0082 | Marine | |
| PAP0083 | Marine | |
| PAP0084 | Marine | |
| PAP0085 | Marine | |
| PAP0086 | Marine | |
| PAP0087 | Mangrove | |
| PAP0088 | Mangrove | |
| PAP0089 | Mangrove | |
| PAP0090 | Mangrove | |
| PAP0091 | Mangrove | |
| PAP0092 | Marine | |
| PAP0093 | Marine | |
| PAP0094 | Marine | |
| PAP0095 | Urban | |
| PAP0096 | Mangrove | |
| PAP0097 | Mangrove | |
| PAP0098 | Urban | |
| PAP0099 | Urban | |
| PAP0100 | Urban | |
| PAP0101 | Urban | |
| PAP0102 | Urban | |
| PAP0103 | Urban | |
| PAP0104 | Urban | |
| PAP0105 | Urban | |
| PAP0106 | Urban | |
| PAP0107 | Urban | |
| PAP0108 | Urban | |
| PAP0109 | Marine | |
| PAP0110 | Urban | |
| PAP0111 | Urban | |
| PAP0112 | Urban | |
| PAP0113 | Urban | |
| PAP0114 | Urban | |
| PAP0115 | Urban | |
| PAP0116 | Urban | |
| PAP0117 | Urban | |
| PAP0118 | Urban | |
| PAP0119 | Urban | |
| PAP0120 | Urban | |
| PAP0121 | Urban | |
| PAP0122 | Urban | |
| PAP0124 | Urban | |
| PAP0125 | Urban | |
| PAP0126 | Urban | |
| PAP0127 | Urban | |
| PAP0128 | Urban | |
| PAP0129 | Urban | |

Do you think you could help me here?

Thanks a lot in advance.

Best,

---

<div class="post-metadata">

**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [October 22, 2025, 5:30pm UTC](https://forum.mothur.org/t/class-is-missing-from-the-lefse-output/22380/2 "2025-10-22T17:30:42Z")

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I’d be happy to help. I am seeing the class displayed when running 1.48.3 with our test data.

 ![Screenshot 2025-10-22 at 1.28.27 PM](https://canada1.discourse-cdn.com/flex036/uploads/mothur/original/1X/1676607e49aa6eeaeaca174424b71031fd9d707e.png)

Could you send your log file, shared file and design file to [mothur.westcott@gmail.com](mailto:mothur.westcott@gmail.com) so I can troubleshoot the issue for you?

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<div class="post-metadata">

**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [October 22, 2025, 9:07pm UTC](https://forum.mothur.org/t/class-is-missing-from-the-lefse-output/22380/3 "2025-10-22T21:07:02Z")

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Thank you for helping us find a bug. Our test files only contain 2 treatments, but your data contains 3 helping me to see the error in the printing of the summary file. I have fixed it and the change will be part of our next release.

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**Author:** ![vherve](https://avatars.discourse-cdn.com/v4/letter/v/b5e925/32.png) [@vherve](https://forum.mothur.org/u/vherve)\
**Post date:** [October 23, 2025, 7:25am UTC](https://forum.mothur.org/t/class-is-missing-from-the-lefse-output/22380/4 "2025-10-23T07:25:51Z")

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Great!  
Do you know when approximately this next release will be? It is just for me to get an idea. In fact, I need to run this analysis on 2 datasets for the revision of a paper. So I would like to know if I can wait a bit or find another solution.  
As a plan B, do you know if I could use an older version of mothur that would work with 3 treatments and on Ubuntu 24.04?

Best,

---

<div class="post-metadata">

**Author:** ![vherve](https://avatars.discourse-cdn.com/v4/letter/v/b5e925/32.png) [@vherve](https://forum.mothur.org/u/vherve)\
**Post date:** [October 23, 2025, 10:32am UTC](https://forum.mothur.org/t/class-is-missing-from-the-lefse-output/22380/5 "2025-10-23T10:32:46Z")

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I just found the answer to my last question: mothur v1.45.0.  
So it will be enough for the revision of my paper!  
Thanks again.

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<div class="post-metadata">

**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\
**Post date:** [November 2, 2025, 10:33am UTC](https://forum.mothur.org/t/class-is-missing-from-the-lefse-output/22380/6 "2025-11-02T10:33:26Z")

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