# \#galaxy-biobakery **URL:** https://help.galaxyproject.org/tag/galaxy-biobakery/211.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [Cannot access the tutorial material to conduct LefSe anaysis on Galaxy](https://help.galaxyproject.org/t/cannot-access-the-tutorial-material-to-conduct-lefse-anaysis-on-galaxy/18454)
**Author:** [@N123](https://help.galaxyproject.org/u/N123)\ **Replies:** 1\ **Last updated:** [October 14, 2026, 6:15pm UTC](https://help.galaxyproject.org/t/cannot-access-the-tutorial-material-to-conduct-lefse-anaysis-on-galaxy/18454 "2026-10-14T18:15:41Z")
Can anyone provide the tutorial materials for conducting LefSe analysis on Galaxy? The tutorial link shows Repository not found. --- ## [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… --- ## [Maaslin2 and maaslin3 errors](https://help.galaxyproject.org/t/maaslin2-and-maaslin3-errors/16258)
**Author:** [@tasha.santiago.bcm](https://help.galaxyproject.org/u/tasha.santiago.bcm)\ **Replies:** 1\ **Last updated:** [September 16, 2025, 11:46pm UTC](https://help.galaxyproject.org/t/maaslin2-and-maaslin3-errors/16258 "2025-09-16T23:46:47Z")
Hi, I’m trying to run maaslin2 and maaslin3 in http://galaxy.biobakery.org/ without any luck. Maaslin2 error says error An error occurred with this dataset: \[1\] “Creating output feature tables folder” \[1\] “Creating out… --- ## [Halla keeps failing even with documents that previously worked](https://help.galaxyproject.org/t/halla-keeps-failing-even-with-documents-that-previously-worked/15990)
**Author:** [@moadlc](https://help.galaxyproject.org/u/moadlc)\ **Replies:** 4\ **Last updated:** [July 17, 2025, 6:39pm UTC](https://help.galaxyproject.org/t/halla-keeps-failing-even-with-documents-that-previously-worked/15990 "2025-07-17T18:39:34Z")
Hello! I am attempting to use the HaLLA service in the Galaxy server. However, even with the default settings, my job keeps failing. I tried using documents that I had previously been able to obtain a hallagram from, but… --- ## [lefse not running?](https://help.galaxyproject.org/t/lefse-not-running/15248)
**Author:** [@EliCas1](https://help.galaxyproject.org/u/EliCas1)\ **Replies:** 3\ **Last updated:** [April 17, 2025, 6:10pm UTC](https://help.galaxyproject.org/t/lefse-not-running/15248 "2025-04-17T18:10:04Z")
I am trying to run Lefse which I have already did successfully many times in the past, BUT now the same identical file is not working anymore… I also tried to use their own example and it fail as well. Did they update th… --- ## [why Galaxy huttenhower lab is not working ?](https://help.galaxyproject.org/t/why-galaxy-huttenhower-lab-is-not-working/10940)
**Author:** [@Ezhil\_Arasi](https://help.galaxyproject.org/u/Ezhil_Arasi)\ **Replies:** 2\ **Last updated:** [February 14, 2025, 9:05pm UTC](https://help.galaxyproject.org/t/why-galaxy-huttenhower-lab-is-not-working/10940 "2025-02-14T21:05:51Z")
I am currently doing lefse analysis. but for the past 4 days, the Galaxy Huttenhower lab page has not opened. says 502 bad gateway --- ## [Format Data for LEfSe](https://help.galaxyproject.org/t/format-data-for-lefse/14725)
**Author:** [@nicollyav](https://help.galaxyproject.org/u/nicollyav)\ **Replies:** 1\ **Last updated:** [February 14, 2025, 12:49am UTC](https://help.galaxyproject.org/t/format-data-for-lefse/14725 "2025-02-14T00:49:04Z")
I’m trying to run analyses with the LEfSe and I’m getting errors. Can anyone help me? These seem to be internal script errors. error An error occurred with this dataset: Traceback (most recent call last): File “/… --- ## [Need Help with Galaxy LEfSe LDA Step Error](https://help.galaxyproject.org/t/need-help-with-galaxy-lefse-lda-step-error/14472)
**Author:** [@jeylee](https://help.galaxyproject.org/u/jeylee)\ **Replies:** 5\ **Last updated:** [January 21, 2025, 8:39pm UTC](https://help.galaxyproject.org/t/need-help-with-galaxy-lefse-lda-step-error/14472 "2025-01-21T20:39:46Z")
Hi, I haven’t used Galaxy LEfSe analysis for a while, and I recently tried to use it again. However, I’m unable to proceed beyond the LDA Effect Size step. I even tested an old text file that worked perfectly a couple of… --- ## [Need Help with Galaxy LEfSe LDA Step Error](https://help.galaxyproject.org/t/need-help-with-galaxy-lefse-lda-step-error/14463)
**Author:** [@jeylee](https://help.galaxyproject.org/u/jeylee)\ **Replies:** 1\ **Last updated:** [January 16, 2025, 6:02pm UTC](https://help.galaxyproject.org/t/need-help-with-galaxy-lefse-lda-step-error/14463 "2025-01-16T18:02:07Z")
Hi, I haven’t used Galaxy LEfSe analysis for a while, and I recently tried to use it again. However, I’m unable to proceed beyond the LDA Effect Size step. I even tested an old text file that worked perfectly a couple of… --- ## [Error while performing LEfSe LDA Effect size](https://help.galaxyproject.org/t/error-while-performing-lefse-lda-effect-size/14196)
**Author:** [@Zbourhane](https://help.galaxyproject.org/u/Zbourhane)\ **Replies:** 1\ **Last updated:** [December 17, 2024, 9:52pm UTC](https://help.galaxyproject.org/t/error-while-performing-lefse-lda-effect-size/14196 "2024-12-17T21:52:58Z")
Hello, I am trying to perform Lefse analysis on http://galaxy.biobakery.org/ as I have done several times before. The first step the format data for lefse is done , but the LDA effect size for data does not work. I have… --- ## [LefSe does not work](https://help.galaxyproject.org/t/lefse-does-not-work/14201)
**Author:** [@samia418](https://help.galaxyproject.org/u/samia418)\ **Replies:** 1\ **Last updated:** [December 17, 2024, 7:29pm UTC](https://help.galaxyproject.org/t/lefse-does-not-work/14201 "2024-12-17T19:29:22Z")
Hi, i can carry out LefSe analysis ,Can anyone tell me when it will be fixed again? this message is displayed We apologize for the inconvinience caused by Galaxy LEfSe and are currently working on fixing the issue. Ple… --- ## [MetaPhlAn Database](https://help.galaxyproject.org/t/metaphlan-database/13443)
**Author:** [@Satomi\_Kohno](https://help.galaxyproject.org/u/Satomi_Kohno)\ **Replies:** 1\ **Last updated:** [September 16, 2024, 6:49pm UTC](https://help.galaxyproject.org/t/metaphlan-database/13443 "2024-09-16T18:49:01Z")
I want to run MetaPhlAn on my local Galaxy to analyze metatranscriptome data, but I don’t know how to set up a database containing clade-specific marker genes. Could you please help me? There are no locally cached datab… --- ## [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… --- ## [Cannot run my workflow for LEfSe](https://help.galaxyproject.org/t/cannot-run-my-workflow-for-lefse/12451)
**Author:** [@Jun](https://help.galaxyproject.org/u/Jun)\ **Replies:** 1\ **Last updated:** [May 8, 2024, 8:11pm UTC](https://help.galaxyproject.org/t/cannot-run-my-workflow-for-lefse/12451 "2024-05-08T20:11:07Z")
I want to compare the gut microbiome of two groups with 16sRNA analysis, using LEfse to make a Figure. I’m updating the text file.A) format data for LEfSe and B) LDA Effect Size proceed fine, but C) Plot LEfse Result see… --- ## [Error in Format Data for LEfSe](https://help.galaxyproject.org/t/error-in-format-data-for-lefse/7746)
**Author:** [@ivanllampy](https://help.galaxyproject.org/u/ivanllampy)\ **Replies:** 2\ **Last updated:** [May 3, 2024, 11:11pm UTC](https://help.galaxyproject.org/t/error-in-format-data-for-lefse/7746 "2024-05-03T23:11:37Z")
Hi all, I am a new user in Galaxy, I am trying to import my 16S dataset for LEfSe. Here is the layout of my dataset: An error then occurs at the “Format Data for LEfSe” stage, as below: I have tried using the Ga… --- ## [LEfSe dataset error report: please give me advice](https://help.galaxyproject.org/t/lefse-dataset-error-report-please-give-me-advice/12267)
**Author:** [@pradit22](https://help.galaxyproject.org/u/pradit22)\ **Replies:** 3\ **Last updated:** [April 24, 2024, 9:25pm UTC](https://help.galaxyproject.org/t/lefse-dataset-error-report-please-give-me-advice/12267 "2024-04-24T21:25:38Z")
Hi everyone, please help me with this matter. Since I’m new here and I tried to upload my data to do LEfSe and follow step in this website: lefse · biobakery/biobakery Wiki · GitHub Then I used my data and it showed as … --- ## [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/… --- ## [LEfSE not working on Galxy module](https://help.galaxyproject.org/t/lefse-not-working-on-galxy-module/12101)
**Author:** [@shahla](https://help.galaxyproject.org/u/shahla)\ **Replies:** 1\ **Last updated:** [April 4, 2024, 5:12pm UTC](https://help.galaxyproject.org/t/lefse-not-working-on-galxy-module/12101 "2024-04-04T17:12:18Z")
I am using teh demo dataset to run LEfSe analysis. The data gets formatted, however the effect size is not calculated. There is an error, when i open to review details of error, following are the detail’s. Is LEfSE worki… --- ## [I am trying to do a cladogram](https://help.galaxyproject.org/t/i-am-trying-to-do-a-cladogram/11729)
**Author:** [@Mai](https://help.galaxyproject.org/u/Mai)\ **Replies:** 3\ **Last updated:** [February 20, 2024, 7:12pm UTC](https://help.galaxyproject.org/t/i-am-trying-to-do-a-cladogram/11729 "2024-02-20T19:12:45Z")
I am trying to do a cladogram with this data but I didn’t get any results, any suggestion? --- ## [Galaxy LEfSe tool](https://help.galaxyproject.org/t/galaxy-lefse-tool/11602)
**Author:** [@celia\_silva](https://help.galaxyproject.org/u/celia_silva)\ **Replies:** 3\ **Last updated:** [January 29, 2024, 11:27pm UTC](https://help.galaxyproject.org/t/galaxy-lefse-tool/11602 "2024-01-29T23:27:13Z")
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 correctl… --- ## [Galaxy hutlab website error](https://help.galaxyproject.org/t/galaxy-hutlab-website-error/11383)
**Author:** [@yiggrite](https://help.galaxyproject.org/u/yiggrite)\ **Replies:** 1\ **Last updated:** [January 6, 2024, 11:17pm UTC](https://help.galaxyproject.org/t/galaxy-hutlab-website-error/11383 "2024-01-06T23:17:16Z")
Hi, Is there something wrong with the Galaxy hutlab website? I could not visit, meeting with the 502 proxy error. Thanks --- ## [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 server is down](https://help.galaxyproject.org/t/lefse-server-is-down/10946)
**Author:** [@salma\_M](https://help.galaxyproject.org/u/salma_M)\ **Replies:** 1\ **Last updated:** [October 12, 2023, 4:32pm UTC](https://help.galaxyproject.org/t/lefse-server-is-down/10946 "2023-10-12T16:32:54Z")
Hello, It has been a week since I have not been able to access the Galaxy public server to run LefSe analysis. Could you please let me know if the server address has changed? Thank you. --- ## [LEfSe: tool request failed](https://help.galaxyproject.org/t/lefse-tool-request-failed/4063)
**Author:** [@Nevenka](https://help.galaxyproject.org/u/Nevenka)\ **Replies:** 2\ **Last updated:** [August 28, 2023, 7:58pm UTC](https://help.galaxyproject.org/t/lefse-tool-request-failed/4063 "2023-08-28T19:58:38Z")
Hi, I’m trying to run the first step of LEfSe microbiome analysis from Huttenhower lab Galaxy on the left menu, running: LEfSe: A) Format data for LEfSe I’m getting the following error for the last two days: “Tool … --- ## [LefSe input file format error](https://help.galaxyproject.org/t/lefse-input-file-format-error/10477)
**Author:** [@esilvaherzog](https://help.galaxyproject.org/u/esilvaherzog)\ **Replies:** 1\ **Last updated:** [July 19, 2023, 7:08pm UTC](https://help.galaxyproject.org/t/lefse-input-file-format-error/10477 "2023-07-19T19:08:22Z")
I am new to Galaxy and have used LefSe through Galaxy before. However, after I upload the file, I get this error --- ## [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… --- ## [probleme with LEfSe](https://help.galaxyproject.org/t/probleme-with-lefse/10268)
**Author:** [@samia418](https://help.galaxyproject.org/u/samia418)\ **Replies:** 1\ **Last updated:** [June 16, 2023, 7:48pm UTC](https://help.galaxyproject.org/t/probleme-with-lefse/10268 "2023-06-16T19:48:47Z")
I can’t finalize my LEfSe, I’d like to know if galaxyHutlab works. here’s the message I get at the second stage of LEFSE can anyone help me, this the message on galaxy hutlab: Error: Cannot count lines in dataset fo… --- ## [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… [Next page](https://help.galaxyproject.org/tag/galaxy-biobakery/211.md?match_all_tags=true&page=1&tags%5B%5D=galaxy-biobakery)