Hello everyone,
I try to have a cladogram with LEfSe. Unfortunately, my output is well a cladogram but it seems that the large highlighted areas do not frame the correct taxa. I’ve tried a lot of options but I dit not find the right.
Second question, I don’t understand why some differently significant species are not highlighted.
Do you have any suggestion for me?
Thanks a lot for your help.
I put you an example here.
Interesting, I haven’t seen this issue before… Are you running this on Galaxy or using the command line?
Thanks,
Meg
Hello again,
Apparently this has happened before, and is due to an issue with the conda environment where the scripts are running. If you make a new, clean conda environment and try running your program, it should fix the issue. Let me know if you still see the issue after that!
Best,
Meg
Hello,
Thanks for your answer. Unfortunately, any suggestions that you give me doesn’t work.
I work on with the shell bash. I remade an clean environment but nothing has changed. I try too on another laptop but it is the same issue.
On Galaxy that’s different because it is unable to produce a graphic. I will try to put my table here 
Best,
Thania
ALL_LEVEL_SAINE_INF.txt (18.1 KB)
Plus, I forgot to tell you that my bash terminal send every time this message :
clade_sep parameter too large, lowered to 0.200225830078
when I run this command line:
lefse_plot_cladogram.py ALL_LEVEL_SAINE_INF.res ALL_LEVEL_SAINE_INF.cladogram.svg --format svg --dpi 600 --title “SAINE_VS_INF”
Thanks
Hi Thaina,
Thanks for the information and the file, I’ll give this a try today and see if I can troubleshoot the problem.
Best,
Meg
Hi Thania,
Thanks for your patience, and I just noticed that I spelled your name incorrectly in my last reply–so sorry about that.
It appears that the accent characters in the “Infectee” labels is causing the problem. I wasn’t able to run LEfSe in Galaxy correctly with your original data, but if I replace the accented characters with non-accented ones, it will run. You may need to create a new conda environment, etc., in order to get the new data to run.
Thanks, and let me know if you’re still seeing problems.
Best,
Meg
Hi Meg,
Thanks a lot for your answer. Indeed, Galaxy works when I suppress the accent, I’m french and it’s difficult for me to totally switch in English , my bad! 
In contrast, this doesn’t solve the problem in command line. So, I’m not able to understand what is the problem 
. However, I’m very happy to know that I could have my cladogramm on galaxy. It’s already a good thing !!
Best,
Thania
Hello, I faced the same error as you - “areas do not frame the correct taxa”. It seems that all the sectors are not centered. Have you managed to resolve it yet?
Hi!
Not at all in command line, however it works on galaxy server…
Indeed! But I prefer using the command-line version.This bug exists in the Python 3-based version of LefSe, whereas the older Python 2-based version does not have this issue. I suggest either using the older version of LefSe directly or, if possible, invoking the older version command when generating the Cladogram plot at the end.
