# Error using lefSe **URL:** \ **Category:** LEfSe\ **Created:** [January 15, 2020, 7:06pm UTC](https://forum.biobakery.org/t/error-using-lefse/142 "2020-01-15T19:06:57Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![sagunmaharjann](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sagunmaharjann/32/168_2.png) [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Post date:** [January 15, 2020, 7:06pm UTC](https://forum.biobakery.org/t/error-using-lefse/142/1 "2020-01-15T19:06:57Z")
From: **Damini** \<[damini@thuenen.de](mailto:damini@thuenen.de)\> I am a PhD student in Germany. In order to analyse my data, I have been trying to use LefSe by accessing the Huttenhower Galaxy Server:[http://huttenhower.sph.harvard.edu/galaxy/](http://huttenhower.sph.harvard.edu/galaxy/) I’m providing the tab limited file following the format of demo file (hmp\_small\_aerobiosis.txt). But, I’m getting the following error Traceback (most recent call last): File “/shed\_tools/[testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format\_input.py](https://urldefense.proofpoint.com/v2/url?u=http-3A__testtoolshed.g2.bx.psu.edu_repos_george-2Dweingart_lefse_a6284ef17bf3_lefse_format-5Finput.py&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=mX4CkpOCZFjfyKKA5iisjoyyOgkllpuCLMUK4n81hm0&m=tLbWQhzAvzoH50q-3Et37zfZwpakbJNkMVm2683590Y&s=zQA1vbYgiTPO1gKOXIBNUE57y2Zeil868YjwSbrd1iE&e=)”, line 429, in class\_sl,subclass\_sl,class\_hierarchy = get\_class\_slices(zip(\*cls.values())) File “/shed\_tools/[testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format\_input.py](https://urldefense.proofpoint.com/v2/url?u=http-3A__testtoolshed.g2.bx.psu.edu_repos_george-2Dweingart_lefse_a6284ef17bf3_lefse_format-5Finput.py&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=mX4CkpOCZFjfyKKA5iisjoyyOgkllpuCLMUK4n81hm0&m=tLbWQhzAvzoH50q-3Et37zfZwpakbJNkMVm2683590Y&s=zQA1vbYgiTPO1gKOXIBNUE57y2Zeil868YjwSbrd1iE&e=)”, line 145, in get\_class\_slices previous\_class = data[0][0] IndexError: list index out of range Could you please suggest, what might be the problem? Or what should I do? Thanks for your help and time. Best regards, Damini Damini Thünen-Institut für Biodiversität Bundesallee 65 38116 Braunschweig Tel. 0531 596 2551 Fax 0531 596 2599 email: [damini@thuenen.de](mailto:damini@thuenen.de) web: [http://www.thuenen.de/de/bd](https://urldefense.proofpoint.com/v2/url?u=http-3A__www.thuenen.de_de_bd&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=mX4CkpOCZFjfyKKA5iisjoyyOgkllpuCLMUK4n81hm0&m=tLbWQhzAvzoH50q-3Et37zfZwpakbJNkMVm2683590Y&s=MMP70AEyiP8cUH7FeSIdkxwPCExK2F7icvUfRMxzoJg&e=) Das Johann Heinrich von Thünen-Institut, Bundesforschungsinstitut für Ländliche Räume, Wald und Fischerei – kurz: Thünen-Institut – besteht aus 14 Fachinstituten, die in den Bereichen Ökonomie, Ökologie und Technologie forschen und die Politik beraten. Damini Thünen Institute of Biodiversity Bundesallee 65 38116 Braunschweig (Germany) Tel: +49 531 596-2551 Fax: +49 531 596-2599 Mail: [damini@thuenen.de](mailto:damini@thuenen.de) Web: [http://www.thuenen.de/en/bd/](https://urldefense.proofpoint.com/v2/url?u=http-3A__www.thuenen.de_en_bd_&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=mX4CkpOCZFjfyKKA5iisjoyyOgkllpuCLMUK4n81hm0&m=tLbWQhzAvzoH50q-3Et37zfZwpakbJNkMVm2683590Y&s=dNdwx7NRuQiuX0fcUYBySzlh1CvOk4pSEIRtJNsLbBI&e=) The Johann Heinrich von Thünen Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries - Thünen Institute in brief - consists of 14 specialized institutes that carry out research and provide policy advice in the fields of economy, ecology and technology. ---
**Author:** ![sma](https://avatars.discourse-cdn.com/v4/letter/s/dec6dc/32.png) [@sma](https://forum.biobakery.org/u/sma)\ **Post date:** [January 22, 2020, 11:04pm UTC](https://forum.biobakery.org/t/error-using-lefse/142/2 "2020-01-22T23:04:27Z")
Hi Damini - My guess is you ran into a formatting error. If you could provide a minimal reproducible dataset that generates the same error (feel free to mask away sensitive info or use toy data), along with your parameter specifications in Galaxy, we’d be glad to help debug the issue! (Also we’d recommend migrating to MaAsLin2 for differential abundance testing - it has friendlier outputs and is more flexible to different testing tasks) Thanks, Siyuan