# \#lefse **URL:** https://help.galaxyproject.org/tag/lefse/114.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [Inclusion of lefse tool for tabular inputs](https://help.galaxyproject.org/t/inclusion-of-lefse-tool-for-tabular-inputs/16351)
**Author:** [@Rachita\_Maruti\_G](https://help.galaxyproject.org/u/Rachita_Maruti_G)\ **Replies:** 1\ **Last updated:** [October 8, 2025, 11:55pm UTC](https://help.galaxyproject.org/t/inclusion-of-lefse-tool-for-tabular-inputs/16351 "2025-10-08T23:55:48Z")
Hi, Right now, Lefse tool in Eu server has the .mothur input format (I have my input in tabular format). Would it possible to add Lefse tool for tabular inputs as it is in biobakery galaxy website which is currently un… --- ## [What should I do to upload the data on LefSe server properly?](https://help.galaxyproject.org/t/what-should-i-do-to-upload-the-data-on-lefse-server-properly/14427)
**Author:** [@Ayushi\_Bhagat](https://help.galaxyproject.org/u/Ayushi_Bhagat)\ **Replies:** 3\ **Last updated:** [January 15, 2025, 7:16pm UTC](https://help.galaxyproject.org/t/what-should-i-do-to-upload-the-data-on-lefse-server-properly/14427 "2025-01-15T19:16:36Z")
Greetings, I am trying to upload my dataset for LefSe and I keep getting the following error. I have tried troubleshooting many times but still it is not moving forward. Can anyone provide any suggestions? Traceback (m… --- ## [Number of significantly discriminative features: 311 ( 311 ) before internal wilcoxon](https://help.galaxyproject.org/t/number-of-significantly-discriminative-features-311-311-before-internal-wilcoxon/13206)
**Author:** [@jianggb](https://help.galaxyproject.org/u/jianggb)\ **Replies:** 2\ **Last updated:** [August 13, 2024, 6:46pm UTC](https://help.galaxyproject.org/t/number-of-significantly-discriminative-features-311-311-before-internal-wilcoxon/13206 "2024-08-13T18:46:22Z")
Hi! I am going to use the LEfSe online analysis function (http://galaxy.biobakery.org/). Step A) went well, but when I got to step B), an error was reported that l do not know how to solve (as follows). l am new in LEfS… --- ## [Error in Lefse LDA Effect Size](https://help.galaxyproject.org/t/error-in-lefse-lda-effect-size/10302)
**Author:** [@icinco](https://help.galaxyproject.org/u/icinco)\ **Replies:** 3\ **Last updated:** [April 8, 2024, 8:46pm UTC](https://help.galaxyproject.org/t/error-in-lefse-lda-effect-size/10302 "2024-04-08T20:46:29Z")
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/… --- ## [Fool seeks aid for Lefsa analysis in Galaxy](https://help.galaxyproject.org/t/fool-seeks-aid-for-lefsa-analysis-in-galaxy/11686)
**Author:** [@dan\_ja](https://help.galaxyproject.org/u/dan_ja)\ **Replies:** 1\ **Last updated:** [February 9, 2024, 7:02pm UTC](https://help.galaxyproject.org/t/fool-seeks-aid-for-lefsa-analysis-in-galaxy/11686 "2024-02-09T19:02:15Z")
Hi all, I’m having some trouble with analysing my sequencing results using Lefsa, I’ve been trying to get my head around all the ways in which I’m getting it wrong but honestly I keep just hitting road blocks, whether i… --- ## [Cannot plot LefSe results](https://help.galaxyproject.org/t/cannot-plot-lefse-results/11201)
**Author:** [@esilvaherzog](https://help.galaxyproject.org/u/esilvaherzog)\ **Replies:** 3\ **Last updated:** [November 29, 2023, 12:49am UTC](https://help.galaxyproject.org/t/cannot-plot-lefse-results/11201 "2023-11-29T00:49:59Z")
Hello , I am using LEfSe analysis for my sequencing data. The data is analyzed, but I cannot see the plot of the results. I am getting this error message: Traceback (most recent call last): File “/usr/bin/lefse\_plot\_… --- ## [LEfSe comparing more than two classes](https://help.galaxyproject.org/t/lefse-comparing-more-than-two-classes/10418)
**Author:** [@microbiome](https://help.galaxyproject.org/u/microbiome)\ **Replies:** 1\ **Last updated:** [July 7, 2023, 5:04pm UTC](https://help.galaxyproject.org/t/lefse-comparing-more-than-two-classes/10418 "2023-07-07T17:04:27Z")
Hi everyone, This is a question for the LEfSe galaxy module: I have a question about comparing more than two classes. Is this possible in the module? I tried this but the results were a bit unexpected. When I compare, … --- ## [Data import LEfSe error: Cannot count lines in file](https://help.galaxyproject.org/t/data-import-lefse-error-cannot-count-lines-in-file/10187)
**Author:** [@garretta](https://help.galaxyproject.org/u/garretta)\ **Replies:** 12\ **Last updated:** [June 20, 2023, 6:35pm UTC](https://help.galaxyproject.org/t/data-import-lefse-error-cannot-count-lines-in-file/10187 "2023-06-20T18:35:13Z")
Hi. I have been using LEfSe in the past and was successfully able to run the full pipeline with the Galaxy LEfSe tool. Now when I am trying to run the pipeline using new tabular files (I believe to be formatted correctly… --- ## [Fatal error: Exit code 1 () on Lefse Galaxy Hub](https://help.galaxyproject.org/t/fatal-error-exit-code-1-on-lefse-galaxy-hub/10204)
**Author:** [@capsola](https://help.galaxyproject.org/u/capsola)\ **Replies:** 1\ **Last updated:** [June 7, 2023, 5:17pm UTC](https://help.galaxyproject.org/t/fatal-error-exit-code-1-on-lefse-galaxy-hub/10204 "2023-06-07T17:17:24Z")
Hello! I am a new user on Galaxy. I wanted to use Lefse to look for differences in my 16S dataset. When I ran the job through, it went well up until B) LDA Effect Size, where I was met with the following error. Fatal e… --- ## [How to fix errors with Lefse](https://help.galaxyproject.org/t/how-to-fix-errors-with-lefse/10183)
**Author:** [@gao](https://help.galaxyproject.org/u/gao)\ **Replies:** 3\ **Last updated:** [June 7, 2023, 4:35pm UTC](https://help.galaxyproject.org/t/how-to-fix-errors-with-lefse/10183 "2023-06-07T16:35:29Z")
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/lefs… --- ## [Failled Data upload](https://help.galaxyproject.org/t/failled-data-upload/9745)
**Author:** [@june](https://help.galaxyproject.org/u/june)\ **Replies:** 6\ **Last updated:** [June 5, 2023, 4:27pm UTC](https://help.galaxyproject.org/t/failled-data-upload/9745 "2023-06-05T16:27:55Z")
Hi There :slight\_smile: When I try uploading Data for the Lefse on the Galaxy / Hutlab server ( Galaxy (harvard.edu)) I get this really weird error, which Ive never gotten before, which I also get with files I know I… --- ## [No results at LEfSe analysis](https://help.galaxyproject.org/t/no-results-at-lefse-analysis/9245)
**Author:** [@m.mihula](https://help.galaxyproject.org/u/m.mihula)\ **Replies:** 1\ **Last updated:** [January 14, 2023, 12:39am UTC](https://help.galaxyproject.org/t/no-results-at-lefse-analysis/9245 "2023-01-14T00:39:39Z")
Dear all, I am using a LEfSe analysis for my sequencing data. I use this format pasted to .tsv file in the notepad: Nevertheless, I do not receive any results. I got that there does not have to be any significant di… --- ## [LEfSe input won't let me choose class row](https://help.galaxyproject.org/t/lefse-input-wont-let-me-choose-class-row/3493)
**Author:** [@Eva](https://help.galaxyproject.org/u/Eva)\ **Replies:** 5\ **Last updated:** [January 2, 2023, 4:17pm UTC](https://help.galaxyproject.org/t/lefse-input-wont-let-me-choose-class-row/3493 "2023-01-02T16:17:10Z")
Hi! I have a problem importing my data to use LEfSe. The file is a tab separated txt file. It won’t let me choose a class row. There is nothing popping up if I click the balk with ‘Choose an option’. Is this an error o… --- ## [Lefse LDA Error "variable 36 appears to be constant within groups"](https://help.galaxyproject.org/t/lefse-lda-error-variable-36-appears-to-be-constant-within-groups/8348)
**Author:** [@Ishanmanandhar](https://help.galaxyproject.org/u/Ishanmanandhar)\ **Replies:** 2\ **Last updated:** [August 4, 2022, 2:30pm UTC](https://help.galaxyproject.org/t/lefse-lda-error-variable-36-appears-to-be-constant-within-groups/8348 "2022-08-04T14:30:20Z")
I have 4 different groups named as group\_1, group\_2, group\_3, and group\_4. 6 samples in each group. The input data was a text file obtained from picrust 2 pathway abundance feature table. I encountered the following erro… --- ## [the way microorganisms are named affect the final results of lefse](https://help.galaxyproject.org/t/the-way-microorganisms-are-named-affect-the-final-results-of-lefse/8337)
**Author:** [@hlsw2001](https://help.galaxyproject.org/u/hlsw2001)\ **Replies:** 5\ **Last updated:** [July 27, 2022, 6:07pm UTC](https://help.galaxyproject.org/t/the-way-microorganisms-are-named-affect-the-final-results-of-lefse/8337 "2022-07-27T18:07:58Z")
Hey, I encountered an issue: I was working on Galaxy and trying to run lefse but the output files were different when I changed the way microorganisms are named. Here is everything that I know: The dataset is green, th… --- ## [Changing feature name changes results in LEfSe](https://help.galaxyproject.org/t/changing-feature-name-changes-results-in-lefse/2989)
**Author:** [@DrNezar](https://help.galaxyproject.org/u/DrNezar)\ **Replies:** 3\ **Last updated:** [July 21, 2022, 5:33pm UTC](https://help.galaxyproject.org/t/changing-feature-name-changes-results-in-lefse/2989 "2022-07-21T17:33:06Z")
I realized LEfSe provides different results from identical data sets in which only feature names have been modified. Compare the outputs below: the number of significant feature differ by 1 and the LDA scores changed for… --- ## [the way features are named affect the final results of lefse](https://help.galaxyproject.org/t/the-way-features-are-named-affect-the-final-results-of-lefse/8338)
**Author:** [@hlsw2001](https://help.galaxyproject.org/u/hlsw2001)\ **Replies:** 1\ **Last updated:** [July 21, 2022, 5:31pm UTC](https://help.galaxyproject.org/t/the-way-features-are-named-affect-the-final-results-of-lefse/8338 "2022-07-21T17:31:23Z")
Hey, I encountered an issue: I was working on Galaxy and trying to run lefse but the output files were different when I changed the way microorganisms are named. Here is everything that I know: The dataset is green, th… --- ## [Lefse Upload File Issue](https://help.galaxyproject.org/t/lefse-upload-file-issue/7518)
**Author:** [@mgcollin19](https://help.galaxyproject.org/u/mgcollin19)\ **Replies:** 0\ **Last updated:** [February 14, 2022, 12:55am UTC](https://help.galaxyproject.org/t/lefse-upload-file-issue/7518 "2022-02-14T00:55:19Z")
Hi All, I have been attempting to upload my data file to Lefse but it will not recognize my microbota data set. I formatted it according to the example file they give but have still not be able to get it to work. I’ve u… --- ## [Display the full name of labels in LEFse cladogram](https://help.galaxyproject.org/t/display-the-full-name-of-labels-in-lefse-cladogram/7289)
**Author:** [@Jen](https://help.galaxyproject.org/u/Jen)\ **Replies:** 4\ **Last updated:** [January 11, 2022, 8:59pm UTC](https://help.galaxyproject.org/t/display-the-full-name-of-labels-in-lefse-cladogram/7289 "2022-01-11T20:59:27Z")
Hi, I could not display the full taxon name of the legend labels on left side of graph while drawing the plot cladogram in LEFse analysis. Some of the indicator/legend labels are as follows. How can I do this? --- ## [Lefse input problem resulting in error "IndexError: list index out of range"](https://help.galaxyproject.org/t/lefse-input-problem-resulting-in-error-indexerror-list-index-out-of-range/6512)
**Author:** [@Emma](https://help.galaxyproject.org/u/Emma)\ **Replies:** 2\ **Last updated:** [September 11, 2021, 3:45am UTC](https://help.galaxyproject.org/t/lefse-input-problem-resulting-in-error-indexerror-list-index-out-of-range/6512 "2021-09-11T03:45:54Z")
I am so sorry to bother you to help me solve this problem. I wanna do the Lefse analysis, the first step of format data seems failed . I can’t get the point about the error. I would be so appreciated if this will be sol… --- ## [Error with 'unexpected input'' when conducting LefSe analysis](https://help.galaxyproject.org/t/error-with-unexpected-input-when-conducting-lefse-analysis/6637)
**Author:** [@smlee-622](https://help.galaxyproject.org/u/smlee-622)\ **Replies:** 2\ **Last updated:** [September 5, 2021, 1:37pm UTC](https://help.galaxyproject.org/t/error-with-unexpected-input-when-conducting-lefse-analysis/6637 "2021-09-05T13:37:58Z")
Hello, Thanks for your development of GALAXY for LefSe analysis. I wanna report my error about ‘unexpected input’. I tried to conduct LefSe analysis with taxa data (exported from Qiime). My data don’t have any subclass… --- ## [Problem with Lefse](https://help.galaxyproject.org/t/problem-with-lefse/5992)
**Author:** [@datle90](https://help.galaxyproject.org/u/datle90)\ **Replies:** 5\ **Last updated:** [May 25, 2021, 5:35pm UTC](https://help.galaxyproject.org/t/problem-with-lefse/5992 "2021-05-25T17:35:46Z")
Hi Sir/Madam, When I try Lefse analysis, I often get this kind of error “Job ran longer than the maximum allowed execution time (runtime: 0:15:15, limit: 00:15:00), please try different inputs or parameters”. Can you… --- ## [Lefse Cladogram isn't complete -- http://huttenhower.sph.harvard.edu/galaxy/](https://help.galaxyproject.org/t/lefse-cladogram-isnt-complete-http-huttenhower-sph-harvard-edu-galaxy/5154)
**Author:** [@arunrr](https://help.galaxyproject.org/u/arunrr)\ **Replies:** 3\ **Last updated:** [May 21, 2021, 6:37am UTC](https://help.galaxyproject.org/t/lefse-cladogram-isnt-complete-http-huttenhower-sph-harvard-edu-galaxy/5154 "2021-05-21T06:37:50Z")
Hi folks, Im new to Galaxy and im running lefse to compare to class(symptomatic and asymptomatic). I get a good differential abundance Lefse results but when plotted, the cladogram looks incomplete(attached). I am not s… --- ## [Problems with Plot Cladogram -- http://huttenhower.sph.harvard.edu/galaxy/](https://help.galaxyproject.org/t/problems-with-plot-cladogram-http-huttenhower-sph-harvard-edu-galaxy/5877)
**Author:** [@liuyushu](https://help.galaxyproject.org/u/liuyushu)\ **Replies:** 1\ **Last updated:** [May 13, 2021, 6:00pm UTC](https://help.galaxyproject.org/t/problems-with-plot-cladogram-http-huttenhower-sph-harvard-edu-galaxy/5877 "2021-05-13T18:00:52Z")
Dear all, I got a weird graphic, and the parameter settings are all default, as follows, what’s the problem,?thank you！ --- ## [If I set the LDA score below the default value of 2.0, is it still statistically reliable?](https://help.galaxyproject.org/t/if-i-set-the-lda-score-below-the-default-value-of-2-0-is-it-still-statistically-reliable/5914)
**Author:** [@Y.D](https://help.galaxyproject.org/u/Y.D)\ **Replies:** 0\ **Last updated:** [May 6, 2021, 2:31pm UTC](https://help.galaxyproject.org/t/if-i-set-the-lda-score-below-the-default-value-of-2-0-is-it-still-statistically-reliable/5914 "2021-05-06T14:31:56Z")
I understood the LEfSe analysis (KW, Wilcoxon), but I am still not sure if I can adjust the default score. Our data shows very few different species for a score\>2.0 . (Independent variable is two, before and after.) So… --- ## [Running 4 lefse analysis at the same time in order to save space for graphic](https://help.galaxyproject.org/t/running-4-lefse-analysis-at-the-same-time-in-order-to-save-space-for-graphic/4838)
**Author:** [@VinceBilly](https://help.galaxyproject.org/u/VinceBilly)\ **Replies:** 2\ **Last updated:** [May 5, 2021, 7:54pm UTC](https://help.galaxyproject.org/t/running-4-lefse-analysis-at-the-same-time-in-order-to-save-space-for-graphic/4838 "2021-05-05T19:54:00Z")
Dear all, I am comparing microbial community in response to a treatment using lefse cladogram. I have 4 different experimental set up and I am planning to display the 4 lefse analysis together in order to compare resul… --- ## [Problems with format data for LEfSe](https://help.galaxyproject.org/t/problems-with-format-data-for-lefse/5847)
**Author:** [@liuyushu](https://help.galaxyproject.org/u/liuyushu)\ **Replies:** 1\ **Last updated:** [April 23, 2021, 10:15pm UTC](https://help.galaxyproject.org/t/problems-with-format-data-for-lefse/5847 "2021-04-23T22:15:54Z")
Dear all: After uploading the data, after format data foe LEfSe, an error is reported, as follows: Traceback (most recent call last): File "/shed\_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a… --- ## [Error message when performing lefse task](https://help.galaxyproject.org/t/error-message-when-performing-lefse-task/5800)
**Author:** [@xkcococo](https://help.galaxyproject.org/u/xkcococo)\ **Replies:** 1\ **Last updated:** [April 16, 2021, 8:56am UTC](https://help.galaxyproject.org/t/error-message-when-performing-lefse-task/5800 "2021-04-16T08:56:38Z")
Hi, I tried to perform a task but I encountered an error message: Traceback (most recent call last): File "/shed\_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format\_input.py", line 4… --- ## [LEfSs uploded file looks different to 2018 – problem?](https://help.galaxyproject.org/t/lefss-uploded-file-looks-different-to-2018-problem/4867)
**Author:** [@janinewaege](https://help.galaxyproject.org/u/janinewaege)\ **Replies:** 2\ **Last updated:** [November 20, 2020, 9:48am UTC](https://help.galaxyproject.org/t/lefss-uploded-file-looks-different-to-2018-problem/4867 "2020-11-20T09:48:21Z")
Hello everyone, I already used LEfSe in 2018 and have now a new dataset to analyse. I noticed when I upload my .tsv file that it looks different when I view the data with the “view data” function (see pictures attached).… --- ## [Legend cut in Lefse Cladogram](https://help.galaxyproject.org/t/legend-cut-in-lefse-cladogram/4820)
**Author:** [@VinceBilly](https://help.galaxyproject.org/u/VinceBilly)\ **Replies:** 5\ **Last updated:** [November 16, 2020, 4:16pm UTC](https://help.galaxyproject.org/t/legend-cut-in-lefse-cladogram/4820 "2020-11-16T16:16:22Z")
Dear All, My Lefse cladogram has an issue. I have too many taxa in the legend and I cannot see all of them. It is like the legend has been cut cause the plot dimension is too small. If you see on the right, my legend … [Next page](https://help.galaxyproject.org/tag/lefse/114.md?match_all_tags=true&page=1&tags%5B%5D=lefse)