# Issues with cladogram.py function **URL:** \ **Category:** LEfSe\ **Created:** [March 18, 2022, 10:38am UTC](https://forum.biobakery.org/t/issues-with-cladogram-py-function/3329 "2022-03-18T10:38:07Z")\ **Posts on this page:** 11\ **Page:** 1
**Author:** ![Thania\_Sbaghdi](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/thania_sbaghdi/32/1331_2.png) [@Thania\_Sbaghdi](https://forum.biobakery.org/u/Thania_Sbaghdi)\ **Post date:** [March 18, 2022, 10:38am UTC](https://forum.biobakery.org/t/issues-with-cladogram-py-function/3329/1 "2022-03-18T10:38:07Z")
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. ![ALL_LEVEL_SAINE_INF.cladogram](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/0/06cd641aac45ab168ed7630fa8d16d8c059d284f.jpeg) ![ALL_LEVEL_SAINE_INF](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/2/2064af5019e66d3970dc85f6d649711409f9b7df.jpeg) ---
**Author:** ![mishort](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mishort/32/556_2.png) [@mishort](https://forum.biobakery.org/u/mishort)\ **Post date:** [March 25, 2022, 7:06pm UTC](https://forum.biobakery.org/t/issues-with-cladogram-py-function/3329/2 "2022-03-25T19:06:20Z")
Interesting, I haven’t seen this issue before… Are you running this on Galaxy or using the command line? Thanks, Meg ---
**Author:** ![mishort](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mishort/32/556_2.png) [@mishort](https://forum.biobakery.org/u/mishort)\ **Post date:** [March 28, 2022, 2:12pm UTC](https://forum.biobakery.org/t/issues-with-cladogram-py-function/3329/3 "2022-03-28T14:12:23Z")
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 ---
**Author:** ![Thania\_Sbaghdi](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/thania_sbaghdi/32/1331_2.png) [@Thania\_Sbaghdi](https://forum.biobakery.org/u/Thania_Sbaghdi)\ **Post date:** [March 28, 2022, 7:45pm UTC](https://forum.biobakery.org/t/issues-with-cladogram-py-function/3329/4 "2022-03-28T19:45:36Z")
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](https://forum.biobakery.org/uploads/short-url/n7Zkr09o4vzXdKJPRiglRzI5wN7.txt) (18.1 KB) ---
**Author:** ![Thania\_Sbaghdi](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/thania_sbaghdi/32/1331_2.png) [@Thania\_Sbaghdi](https://forum.biobakery.org/u/Thania_Sbaghdi)\ **Post date:** [March 29, 2022, 9:37am UTC](https://forum.biobakery.org/t/issues-with-cladogram-py-function/3329/5 "2022-03-29T09:37:19Z")
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 🙂 ---
**Author:** ![mishort](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mishort/32/556_2.png) [@mishort](https://forum.biobakery.org/u/mishort)\ **Post date:** [March 29, 2022, 3:20pm UTC](https://forum.biobakery.org/t/issues-with-cladogram-py-function/3329/6 "2022-03-29T15:20:14Z")
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 ---
**Author:** ![mishort](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mishort/32/556_2.png) [@mishort](https://forum.biobakery.org/u/mishort)\ **Post date:** [March 30, 2022, 8:37pm UTC](https://forum.biobakery.org/t/issues-with-cladogram-py-function/3329/7 "2022-03-30T20:37:43Z")
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 ---
**Author:** ![Thania\_Sbaghdi](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/thania_sbaghdi/32/1331_2.png) [@Thania\_Sbaghdi](https://forum.biobakery.org/u/Thania_Sbaghdi)\ **Post date:** [March 31, 2022, 8:42am UTC](https://forum.biobakery.org/t/issues-with-cladogram-py-function/3329/8 "2022-03-31T08:42:41Z")
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 ---
**Author:** ![RChGO](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/rchgo/32/553_2.png) [@RChGO](https://forum.biobakery.org/u/RChGO)\ **Post date:** [June 5, 2023, 5:03am UTC](https://forum.biobakery.org/t/issues-with-cladogram-py-function/3329/9 "2023-06-05T05:03:12Z")
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? ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/a/a735678f6727aaff79a94e3096bda3d9bcf0aa9e.png) ---
**Author:** ![Thania\_Sbaghdi](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/thania_sbaghdi/32/1331_2.png) [@Thania\_Sbaghdi](https://forum.biobakery.org/u/Thania_Sbaghdi)\ **Post date:** [June 8, 2023, 6:46am UTC](https://forum.biobakery.org/t/issues-with-cladogram-py-function/3329/10 "2023-06-08T06:46:37Z")
Hi! Not at all in command line, however it works on galaxy server… ---
**Author:** ![RChGO](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/rchgo/32/553_2.png) [@RChGO](https://forum.biobakery.org/u/RChGO)\ **Post date:** [June 9, 2023, 12:44pm UTC](https://forum.biobakery.org/t/issues-with-cladogram-py-function/3329/11 "2023-06-09T12:44:36Z")
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.