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

Downstream analysis and statistics LEfSe
1

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

2

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