Hi!! Sorry my student was just able to run this LefSe again on the updated 1.47 version of mothur but we’re still not getting the class values in the output. I’ve included the log and part of the output in case we’re missing 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 |