LEfSe - Cladogram missing legend

I am running the LEfSe module locally. I am attempting to process and plot my data, but I’m not getting a legend when I plot the cladogram. I suspect this may be due to the class/group names being incorrectly processed. I

The top of my data file looks like this:

Group 1 2 1 2 1 2 2 1 2 1 2 2 1 1 1
name JYL_7_1_2_L001_R1_001 JYL_6_1_1_L001_R1_001 JYL_10_1_5_L001_R1_001 JYL_5_2_0_L001_R1_001 JYL_9_3_4_L001_R1_001 JYL_9_1_3_L001_R1_001 JYL_10_4_6_L001_R1_001 JYL_15_1_8_L001_R1_001 JYL_13_1_7_L001_R1_001 JYL_26_1_11_L001_R1_001 JYL_26_3_12_L001_R1_001 JYL_18_1_9_L001_R1_001 JYL_28_1_13_L001_R1_001 JYL_33_1_14_L001_R1_001 JYL_24_1_10_L001_R1_001
Bacteria Actinobacteria 33219 20022 8300 2237 9476 16156 15016 1148 11127 2168 2417 2870 18122 8260
Bacteria Bacteroidetes 2724 8166 2475 16820 6528 3423 10939 14979 8868 2932 30961 4377 673 1700

I have processed my data using lefse_format_input.py with these flags “-c 1 -u 2 -o 1000000” and then executed lefse_run.py to create the .res file.

Here is the top of the resulting .res file:

Bacteria.Actinobacteria 4.310612689030659 -
Bacteria.Bacteroidetes 4.363902188063198 -
Bacteria.Chlamydiae 0.23186646960619614 -
Bacteria.Cyanobacteria 1.1029480902342559 -
Bacteria.Deferribacteres 0.6616523706543642 -

I noticed that each line ends with a “-” rather than a group label, but I’m not sure if that’s what’s causing the issue with the missing legend.

Any advice?

Consolidating into → Need Help with Galaxy LEfSe LDA Step Error

Let’s keep your question in a single topic instead of breaking up into so many repeated questions across topics.

You can clarify in that other topic about how you are “using the tool locally”. If this is in a Galaxy server, then the version of Galaxy you are running will be relevant along with how/where you installed the tool, then details about the tool version and usage I listed out there.

Thanks! :slight_smile: