# LEfSe issues and errors **URL:** \ **Category:** LEfSe\ **Created:** [June 5, 2023, 6:27pm UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397 "2023-06-05T18:27:50Z")\ **Posts on this page:** 20\ **Page:** 2
**Author:** ![Kevin\_Ketagoda](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/kevin_ketagoda/32/2509_2.png) [@Kevin\_Ketagoda](https://forum.biobakery.org/u/Kevin_Ketagoda)\ **Post date:** [October 27, 2023, 4:12am UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397/21 "2023-10-27T04:12:42Z")
Hi @sagunmaharjann I still keep getting this error and I am unable to generate the LDA plots. Kind regards Kevin ---
**Author:** ![AMMC](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/ammc/32/2736_2.png) [@AMMC](https://forum.biobakery.org/u/AMMC)\ **Post date:** [February 23, 2024, 10:11am UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397/22 "2024-02-23T10:11:55Z")
Hello, I am trying to run LEfSe now and I have the same problem and message that you commented before in this conversation. Id the problem with maintenance unsolved yet? Error message: Number of significantly discriminative features: 57 ( 57) before internal wilcoxon Traceback (most recent call last): File “/galaxy\_venv/bin/lefse\_run.py”, line 33, in sys.exit(load\_entry\_point(‘lefse==1.1.2’, ‘console\_scripts’, 'lefse\_ru Thank you very much in advance! ---
**Author:** ![Santiago\_CR](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/santiago_cr/32/2743_2.png) [@Santiago\_CR](https://forum.biobakery.org/u/Santiago_CR)\ **Post date:** [February 26, 2024, 5:42am UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397/24 "2024-02-26T05:42:41Z")
I am having the same problem too… Number of significantly discriminative features: 4 ( 38 ) before internal wilcoxon Traceback (most recent call last): File “/galaxy\_venv/bin/lefse\_run.py”, line 33, in sys.exit(load\_entry\_point(‘lefse==1.1.2’, ‘console\_scripts’, 'lefse\_run And I am using an old dataset that were previously working ☹ ---
**Author:** ![bseiber3](https://avatars.discourse-cdn.com/v4/letter/b/f14d63/32.png) [@bseiber3](https://forum.biobakery.org/u/bseiber3)\ **Post date:** [February 28, 2024, 4:20pm UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397/25 "2024-02-28T16:20:24Z")
I am also having the same problem with an old dataset that previously worked. Thank you so much for all your help! Number of significantly discriminative features: 16 ( 16 ) before internal wilcoxon Traceback (most recent call last): File “/galaxy\_venv/bin/lefse\_run.py”, line 33, in sys.exit(load\_entry\_point(‘lefse==1.1.2’, ‘console\_scripts’, 'lefse\_ru ---
**Author:** ![TMM](https://avatars.discourse-cdn.com/v4/letter/t/85e7bf/32.png) [@TMM](https://forum.biobakery.org/u/TMM)\ **Post date:** [February 28, 2024, 5:38pm UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397/26 "2024-02-28T17:38:15Z")
Hello, I am having also the same problem with a dataset that worked previously. Number of significantly discriminative features: 12 ( 12 ) before internal wilcoxon Traceback (most recent call last): File “/galaxy\_venv/bin/lefse\_run.py”, line 33, in sys.exit(load\_entry\_point(‘lefse==1.1.2’, ‘console\_scripts’, 'lefse\_ru Is it a problem with maintenance? When will this be resolved? Thank you in advance! ---
**Author:** ![AngelSoto](https://avatars.discourse-cdn.com/v4/letter/a/46a35a/32.png) [@AngelSoto](https://forum.biobakery.org/u/AngelSoto)\ **Post date:** [February 28, 2024, 6:10pm UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397/27 "2024-02-28T18:10:31Z")
Hi, I am having the same problem, this will be resolved? ---
**Author:** ![Allan\_Amorim\_Santos](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/allan_amorim_santos/32/2753_2.png) [@Allan\_Amorim\_Santos](https://forum.biobakery.org/u/Allan_Amorim_Santos)\ **Post date:** [February 28, 2024, 11:54pm UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397/28 "2024-02-28T23:54:54Z")
Hi everyone, I’m facing the same issue from here on using lefse tool. Anyone can help me with this? thanks ---
**Author:** ![Nimisha\_Nimisha](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nimisha_nimisha/32/2772_2.png) [@Nimisha\_Nimisha](https://forum.biobakery.org/u/Nimisha_Nimisha)\ **Post date:** [March 14, 2024, 6:40pm UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397/29 "2024-03-14T18:40:32Z")
Hi all, I am having the same issue. Was this resolved for anyone recently? Traceback (most recent call last): File “/galaxy\_venv/bin/lefse\_format\_input.py”, line 33, in sys.exit(load\_entry\_point(‘lefse==1.1.2’, ‘console\_scripts’, ‘lefse\_format\_input.py’)()) File “/galaxy\_venv/lib/python3.7/site-packages/lefse-1.1.2-py3.7.egg/lefse/lefse\_format\_input.py”, line 439, in format\_input File “/galaxy\_venv/lib/python3.7/site-packages/lefse-1.1.2-py3.7.egg/lefse/lefse\_format\_input.py”, line 163, in get\_class\_slices IndexError: list index out of range Thanks ---
**Author:** ![Letizia\_Iuffrida](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/letizia_iuffrida/32/2777_2.png) [@Letizia\_Iuffrida](https://forum.biobakery.org/u/Letizia_Iuffrida)\ **Post date:** [March 19, 2024, 2:50am UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397/30 "2024-03-19T02:50:28Z")
Hello everyone, I’m trying to run LEfSE analysis on some genes data and for some reason I am unable to continue due to this error during step 3: Traceback (most recent call last): File “/galaxy\_venv/bin/lefse\_run.py”, line 33, in sys.exit(load\_entry\_point(‘lefse==1.1.2’, ‘console\_scripts’, ‘lefse\_run.py’)()) File “/galaxy\_venv/lib/python3.7/site-packages/lefse-1.1.2-py3.7.egg/lefse/lefse\_run.py”, line 90, in lefse\_run File “/galaxy\_venv/lib/python3.7/site-packages/lefse-1.1.2-py3.7.egg/lefse/lefse.py”, line 225, in test\_lda\_r AttributeError: ‘NoneType’ object has no attribute ‘rownames’ Can someone give me a help? I’m pretty stuck. This is the input file: [LefSE.txt](https://forum.biobakery.org/uploads/short-url/y4zvUppI32I8Gg0q4UPINaUiyzt.txt) (2.5 KB) ---
**Author:** ![shahla](https://avatars.discourse-cdn.com/v4/letter/s/97f17d/32.png) [@shahla](https://forum.biobakery.org/u/shahla)\ **Post date:** [April 4, 2024, 5:50pm UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397/31 "2024-04-04T17:50:38Z")
I am trying to use LEfSE , using the demo dataset. However getting error in calculating effect size (step 3).Here is the error. please help. 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 ---
**Author:** ![redida01](https://avatars.discourse-cdn.com/v4/letter/r/977dab/32.png) [@redida01](https://forum.biobakery.org/u/redida01)\ **Post date:** [April 21, 2024, 11:59pm UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397/32 "2024-04-21T23:59:49Z")
[Lefse-CDV-level-4.txt](https://forum.biobakery.org/uploads/short-url/sowdNB7sMlxdr2VgC5KKRDnYJBF.txt) (9.6 KB) I’m unable to get the LDA Effect Size tool to run in Lefse. I get this error message: ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/9/90ee4a1ebf67e7327310075f14445b36755a17f8.png) ---
**Author:** ![Bianca\_Costa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/bianca_costa/32/2831_2.png) [@Bianca\_Costa](https://forum.biobakery.org/u/Bianca_Costa)\ **Post date:** [April 24, 2024, 2:14am UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397/33 "2024-04-24T02:14:49Z")
Hi, I am new to running lefse and I was trying out the galaxy interface to run the sample data but it failed on the second step-B) LDA effect size (LEfSe) -see text below Can you advise if this is a program-wide issue or if I am doing something wrong in following the protocol? thank you! Traceback (most recent call last): File “/galaxy\_venv/bin/lefse\_run.py”, line 33, in ‹module\> sys.exit(load\_entry\_point(‘lefse=-1.1.2’, 'console\_scripts", “lefse\_run.py”)()) File “/galaxy\_venv/lib/python3.7/site-packages/lefse-1.1.2-py3.7.egg/lefse/lefse\_run.py”, line 90, in lefse\_run File “/galaxy\_venv/lib/python3.7/site-packages/lefse-1.1.2-py3.7.egg/lefse/lefse.py”,line 225, in test\_Ida\_r AttributeError: ‘NoneTvpe’ obiect has no attribute 'rownames" ---
**Author:** ![Natasha](https://avatars.discourse-cdn.com/v4/letter/n/df705f/32.png) [@Natasha](https://forum.biobakery.org/u/Natasha)\ **Post date:** [May 2, 2024, 12:28pm UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397/34 "2024-05-02T12:28:23Z")
Hi, I am having the same issue with LefSe analysis. Has anyone been able to sort the issue??? Traceback (most recent call last): File “/galaxy\_venv/bin/lefse\_run.py”, line 33, in sys.exit(load\_entry\_point(‘lefse==1.1.2’, ‘console\_scripts’, ‘lefse\_run.py’)()) File “/galaxy\_venv/lib/python3.7/site-packages/lefse-1.1.2-py3.7.egg/lefse/lefse\_run.py”, line 90, in lefse\_run File “/galaxy\_venv/lib/python3.7/site-packages/lefse-1.1.2-py3.7.egg/lefse/lefse.py”, line 225, in test\_lda\_r AttributeError: ‘NoneType’ object has no attribute ‘rownames’ error An error occurred with this dataset: Number of significantly discriminative features: 1 ( 16 ) before internal wilcoxon Traceback (most recent call last): File “/galaxy\_venv/bin/lefse\_run.py”, line 33, in sys.exit(load\_entry\_point(‘lefse==1.1.2’, ---
**Author:** ![Allan\_Amorim\_Santos](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/allan_amorim_santos/32/2753_2.png) [@Allan\_Amorim\_Santos](https://forum.biobakery.org/u/Allan_Amorim_Santos)\ **Post date:** [May 3, 2024, 8:56pm UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397/35 "2024-05-03T20:56:35Z")
Anyone can help us with these issue? thanks ---
**Author:** ![garretta](https://avatars.discourse-cdn.com/v4/letter/g/ecccb3/32.png) [@garretta](https://forum.biobakery.org/u/garretta)\ **Post date:** [November 17, 2024, 12:12am UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397/36 "2024-11-17T00:12:34Z")
Hi @sagunmaharjann I cannot ignore this issue as it won’t let me use the error dataset in the pipeline. Is there any update on the resolve? ---
**Author:** ![xinxin](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/xinxin/32/3095_2.png) [@xinxin](https://forum.biobakery.org/u/xinxin)\ **Post date:** [December 5, 2024, 7:03am UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397/37 "2024-12-05T07:03:45Z")
Hi! I met the same error when I used LEfSe. I run into one error in Step B) Error message: Number of significantly discriminative features: 36 ( 36 ) before internal wilcoxon Traceback (most recent call last): File “/galaxy\_venv/bin/lefse\_run.py”, line 33, in sys.exit(load\_entry\_point(‘lefse==1.1.2’, ‘console\_scripts’, 'lefse\_ru I have tried to resolve these problems many different ways, but i did not resolve it. It is greatly appreciated for any help. Thanks a lot! ---
**Author:** ![Zee](https://avatars.discourse-cdn.com/v4/letter/z/df788c/32.png) [@Zee](https://forum.biobakery.org/u/Zee)\ **Post date:** [December 17, 2024, 1:40pm UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397/38 "2024-12-17T13:40:11Z")
Hi @Kelsey_Thompson, i have the same problem. I am trying to run the pipeline using new tabular files (I believe to be formatted correctly) and even old ones that successfully worked in the past. I have this error: Any recommandation ? thank you Fatal error: Exit code 1 () Tool generated the following standard error: ```auto Traceback (most recent call last): File "/galaxy_venv/bin/lefse_run.py", line 33, in sys.exit(load_entry_point('lefse==1.1.2', 'console_scripts', 'lefse_run.py')()) File "/galaxy_venv/lib/python3.7/site-packages/lefse-1.1.2-py3.7.egg/lefse/lefse_run.py", line 90, in lefse_run File "/galaxy_venv/lib/python3.7/site-packages/lefse-1.1.2-py3.7.egg/lefse/lefse.py", line 225, in test_lda_r ``` AttributeError: ‘NoneType’ object has no attribute ‘rownames’ ---
**Author:** ![Sam\_Elkins](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sam_elkins/32/3139_2.png) [@Sam\_Elkins](https://forum.biobakery.org/u/Sam_Elkins)\ **Post date:** [February 7, 2025, 5:05pm UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397/39 "2025-02-07T17:05:25Z")
Hello, I am a new user to this program and I am currently working through the [tutorial](https://github.com/biobakery/biobakery/wiki/lefse) for lefse. I have received an error on the B) LDA Effect Size (LEfSe) step. The error says “number of significant discriminating features: 8 (131) before internal wilcoxon”. I have checked to make sure I’m not doing anything obvious to be getting this error however I have been unable to solve it. I’ve searched this error up online and similar results are found when there is a bug in the server, and I did not see any solution so I can be done on my end. Can you think of anything that can be done? ---
**Author:** ![kadunn](https://avatars.discourse-cdn.com/v4/letter/k/ee59a6/32.png) [@kadunn](https://forum.biobakery.org/u/kadunn)\ **Post date:** [February 14, 2025, 2:30pm UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397/40 "2025-02-14T14:30:21Z")
Hi This seems to still be an unfixed issue are there any updates? Old files that ran and results were published now don’t work. Has the input format changed? Thanks ---
**Author:** ![nataliauni](https://avatars.discourse-cdn.com/v4/letter/n/f1d935/32.png) [@nataliauni](https://forum.biobakery.org/u/nataliauni)\ **Post date:** [March 13, 2025, 7:50pm UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397/41 "2025-03-13T19:50:32Z")
Hello! I keep getting this error when running **A) Format Data for LEfSe** (Galaxy Version 1.0) Details Execution resulted in the following messages: Fatal error: Exit code 1 () Tool generated the following standard error: Traceback (most recent call last): File “/galaxy\_venv/bin/lefse\_format\_input.py”, line 33, in sys.exit(load\_entry\_point(‘lefse==1.1.2’, ‘console\_scripts’, ‘lefse\_format\_input.py’)()) File “/galaxy\_venv/bin/lefse\_format\_input.py”, line 25, in importlib\_load\_entry\_point return next(matches).load() File “/galaxy\_venv/lib/python3.7/site-packages/importlib\_metadata/ **init**.py”, line 96, in load module = import\_module(match.group(‘module’)) File “/tool\_deps/\_conda/lib/python3.7/importlib/ **init**.py”, line 127, in import\_module return \_bootstrap.\_gcd\_import(name[level:], package, level) File “”, line 1006, in \_gcd\_import File “”, line 983, in \_find\_and\_load File “”, line 967, in \_find\_and\_load\_unlocked File “”, line 668, in \_load\_unlocked File “”, line 638, in \_load\_backward\_compatible File “/galaxy\_venv/lib/python3.7/site-packages/lefse-1.1.2-py3.7.egg/lefse/lefse\_format\_input.py”, line 7, in **requires** = ‘lefse==1.1.2’ File “”, line 983, in \_find\_and\_load File “”, line 967, in \_find\_and\_load\_unlocked File “”, line 668, in \_load\_unlocked File “”, line 638, in \_load\_backward\_compatible File “/galaxy\_venv/lib/python3.7/site-packages/lefse-1.1.2-py3.7.egg/lefsebiom/AbundanceTable.py”, line 54, in File “/galaxy\_venv/lib/python3.7/site-packages/biom/ **init**.py”, line 51, in from .table import Table File “/galaxy\_venv/lib/python3.7/site-packages/biom/table.py”, line 196, in from .\_filter import \_filter File “biom/\_filter.pyx”, line 1, in init biom.\_filter ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject [Previous page](https://forum.biobakery.org/t/lefse-issues-and-errors/5397.md?page=1)