# Lefse error conda install -c bioconda/label/cf201901 lefse

**URL:** <https://forum.biobakery.org/t/lefse-error-conda-install-c-bioconda-label-cf201901-lefse/352>\
**Category:** LEfSe\
**Created:** [April 18, 2020, 8:49pm UTC](https://forum.biobakery.org/t/lefse-error-conda-install-c-bioconda-label-cf201901-lefse/352 "2020-04-18T20:49:21Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Anushka\_Khasnobish](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/anushka_khasnobish/32/131_2.png) [@Anushka\_Khasnobish](https://forum.biobakery.org/u/Anushka_Khasnobish)\
**Post date:** [April 18, 2020, 8:49pm UTC](https://forum.biobakery.org/t/lefse-error-conda-install-c-bioconda-label-cf201901-lefse/352/1 "2020-04-18T20:49:21Z")

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Being a new user on this forum, I am unable to upload files. I have been using the Lefse tool on huttenhowerDOTsphDOTharvardDOTedu/galaxy platform. I was able to process all my files using this tool but at the species level abundance, when I used my input file (.txt extension; format: tabular) , **[A) Format Data for LEfSe]** worked perfectly but **[B)LDA effect size (LefSe)]** when run with default parameters gave me the following error:

Dataset 13: B) LDA Effect Size (LEfSe) on data 12

Tool execution generated the following error message:  
/galaxy\_venv/local/lib/python2.7/site-packages/rpy2/rinterface/ **init**.py:185: RRuntimeWarning: Error in (function (file = “”, n = NULL, text = NULL, prompt = “?”, keep.source = getOption(“keep.source”), :  
:1:435: unexpected input  
1: bacteriumacnes + Haemophilusparahaemolyticus + Selenomonassp\_oralcloneGI064 + Romboutsiailealis + Porphyromonassp\_oralcloneCW034 + Stomatobaculumlongum + Solobacteriummoorei + unculturedPrevot  
^

warnings.warn(x, RRuntimeWarning)  
Traceback (most recent call last):  
File “/shed\_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/run\_lefse.py”, line 89, in   
if params[‘rank\_tec’] == ‘lda’: lda\_res,lda\_res\_th = test\_lda\_r(cls,feats,class\_sl,params[‘n\_boots’],params[‘f\_boots’],params[‘lda\_abs\_th’],0.0000000001,params[‘nlogs’])  
File “/export/shed\_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/lefse.py”, line 189, in test\_lda\_r  
z = robjects.r(‘z \<- suppressWarnings(lda(as.formula(’+f+’),data=sub\_d,tol=’+str(tol\_min)+’))’)  
File “/galaxy\_venv/local/lib/python2.7/site-packages/rpy2/robjects/ **init**.py”, line 358, in **call**  
p = \_rparse(text=StrSexpVector((string,)))  
rpy2.rinterface.RRuntimeError: Error in (function (file = “”, n = NULL, text = NULL, prompt = “?”, keep.source = getOption(“keep.source”), :  
:1:435: unexpected input  
1: bacteriumacnes + Haemophilusparahaemolyticus + Selenomonassp\_oralcloneGI064 + Romboutsiailealis + Porphyromonassp\_oralcloneCW034 + Stomatobaculumlongum + Solobacteriummoorei + unculturedPrevot  
^

The tool produced the following additional output:  
Number of significantly discriminative features: 32 ( 32 ) before internal wilcoxon

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**Author:** ![sma](https://avatars.discourse-cdn.com/v4/letter/s/dec6dc/32.png) [@sma](https://forum.biobakery.org/u/sma)\
**Post date:** [April 24, 2020, 3:37pm UTC](https://forum.biobakery.org/t/lefse-error-conda-install-c-bioconda-label-cf201901-lefse/352/2 "2020-04-24T15:37:51Z")

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Hi,

It’s a bit hard to debug the error without input files. Could you share them through email? Feel free to subset/mask sensitive fields as long as it produces the same error. You can reach me at siyuanma@g.harvard.edu.

Thanks,  
Siyuan