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??
LOG
Mac version
Using ReadLine,Boost,HDF5,GSL
mothur v.1.47.0
Last updated: 1/21/22
by
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 https://forum.mothur.org
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, design=healthy.status.design)
You did not provide a class, using Horse.
0.03
Number of significantly discriminative features: 1676 ( 3788 ) before internal wilcoxon.
Number of discriminative features with abs LDA score > 2 : 697.
Output File Names:
stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.subsample.0.03.lefse_summary
mothur > quit()
Logfile : mothur.1644603149.logfile
OUTPUT
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 |