# Error in Lefse LDA Effect Size **URL:** \ **Category:** Uncategorized\ **Tags:** lefse, galaxy-biobakery\ **Created:** [June 21, 2023, 1:54pm UTC](https://help.galaxyproject.org/t/error-in-lefse-lda-effect-size/10302 "2023-06-21T13:54:52Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![icinco](https://avatars.discourse-cdn.com/v4/letter/i/df788c/32.png) [@icinco](https://help.galaxyproject.org/u/icinco)\ **Post date:** [June 21, 2023, 1:54pm UTC](https://help.galaxyproject.org/t/error-in-lefse-lda-effect-size/10302/1 "2023-06-21T13:54:52Z")
I generated a new data.txt and successfully uploaded and formatted the data set. However, when running LDA Effect Size, I received the following traceback error: Traceback (most recent call last): File “/usr/local/bin/lefse\_run.py”, line 5, in from lefse.lefse\_run import lefse\_run File “/usr/local/lib/python2.7/dist-packages/lefse/lefse\_run.py”, line 4, in from lefse.lefse import \* ImportError: No module named lefse To be safe, I re-uploaded a .txt file that I successfully ran in the past and received the same traceback error. The last line, “ImportError: No module named lefse” makes me think that there was an issue with the command line itself rather than my file. Please advise. Thank you. ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [June 21, 2023, 7:06pm UTC](https://help.galaxyproject.org/t/error-in-lefse-lda-effect-size/10302/2 "2023-06-21T19:06:46Z")
Welcome, @icinco Let’s consolidate this with the primary thread about the topic. Details, including a link to the admins that run that server, are included. [Data import LEfSe error: Cannot count lines in file - #11 by jennaj](https://help.galaxyproject.org/t/data-import-lefse-error-cannot-count-lines-in-file/10187/11) ---
**Author:** ![shahla](https://avatars.discourse-cdn.com/v4/letter/s/97f17d/32.png) [@shahla](https://help.galaxyproject.org/u/shahla)\ **Post date:** [April 4, 2024, 4:50pm UTC](https://help.galaxyproject.org/t/error-in-lefse-lda-effect-size/10302/3 "2024-04-04T16:50:15Z")
I am trying to use the demo dataset -hmp\_aerobiosis\_small. However LeFSE continues to fail. here is the error-B) LDA Effect Size (LEfSe) Dataset Information Number: 30 Name: B) LDA Effect Size (LEfSe) on data 24 Created: Thu Apr 4 06:59:52 2024 (UTC) Filesize: 0 bytes Dbkey: ? Format: lefse\_internal\_res Job Information Galaxy Tool ID: LEfSe\_run Galaxy Tool Version: 1.0 Tool Version: Tool Standard Output: stdout Tool Standard Error: stderr Tool Exit Code: 1 Job Messages Fatal error: Exit code 1 () History Content API ID: 702897e66004936f Job API ID: 45c670429e65ac89 History API ID: 22bdbe9d6e0775fe UUID: 1d91591b-9502-42d7-8a9c-75673abcb8e5 Tool Parameters Input Parameter Value Select data 24: A) Format Data for LEfSe on data 22 Alpha value for the factorial Kruskal-Wallis test among classes 0.05 Alpha value for the pairwise Wilcoxon test between subclasses 0.05 Threshold on the logarithmic LDA score for discriminative features 2.0 Do you want the pairwise comparisons among subclasses to be performed only among the subclasses with the same name? No Set the strategy for multi-class analysis All-against-all (more strict) Inheritance Chain B) LDA Effect Size (LEfSe) on data 24 Dataset peek no peek. Please help. ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [April 8, 2024, 8:46pm UTC](https://help.galaxyproject.org/t/error-in-lefse-lda-effect-size/10302/4 "2024-04-08T20:46:29Z")
> [@LEfSE not working on Galxy module](https://help.galaxyproject.org/t/lefse-not-working-on-galxy-module/12101/2): > > We cannot provide much help with issues specific to LEfSE tools not working, unfortunately. Your best chance is to try to contact someone that maintains the lefse galaxy server, possibly at [https://forum.biobakery.org/](https://forum.biobakery.org/). ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [April 8, 2024, 8:46pm UTC](https://help.galaxyproject.org/t/error-in-lefse-lda-effect-size/10302/5 "2024-04-08T20:46:37Z")