Still struggling with LefSe v 1.47 no class

Hi!! Sorry for the struggles but I’m still getting no class values in the output when I run LefSe again on the updated 1.47 version of mothur. I’ve tried re-downloading it but still gives me the same output so I’m pretty sure it’s in the version, I’ve also checked the supplemental data on the command in case something was added in but I’m pretty sure that the command I’m running is right. I’ve included the log and part of the output in case I’m missing a piece of the code or something!! Any ideas??


Mac version

Using ReadLine,Boost,HDF5,GSL
mothur v.1.47.0
Last updated: 1/21/22
Patrick D. Schloss

Department of Microbiology & Immunology

University of Michigan

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type ‘help()’ for information on the commands that are available

For questions and analysis support, please visit our forum at

Type ‘quit()’ to exit program

[NOTE]: Setting random seed to 19760620.

Interactive Mode

mothur > lefse(shared=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.subsample.shared,

You did not provide a class, using Horse.


Number of significantly discriminative features: 1676 ( 3788 ) before internal wilcoxon.
Number of discriminative features with abs LDA score > 2 : 697.

Output File Names:

mothur > quit()
Logfile : mothur.1644603149.logfile


OTU logMaxMean LDA pValue
Otu00001 4.63535 4.15518 0.00547327
Otu00002 4.63602 4.14292 0.0047793
Otu00003 4.9219 NA NA
Otu00004 4.36013 NA NA
Otu00005 4.06121 3.60389 0.000888753
Otu00006 4.24132 3.80731 0.0002196
Otu00007 4.35071 4.01646 5.88673e-06
Otu00008 4.10149 3.58508 0.01029
Otu00009 4.2222 3.91117 0.000108709
Otu00010 4.10926 3.71313 0.000254189
Otu00011 4.03043 3.80899 0.000448923
Otu00012 4.27474 NA NA
Otu00013 4.17678 3.81173 5.44742e-05
Otu00014 4.19785 3.8552 0.000174323

Could you send your shared and design file to

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