Dataset 66: B) LDA Effect Size (LEfSe) on data 65
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”), :
:1:373: unexpected input
1: s + Erythrobacter + Aeromicrobium + Renibacterium + Anaerosalibacter + Parvibaculum + Lachnospiraceae_NC2004_group + Finegoldia + Phascolarctobacterium + Ancylobacter + uncultured_bacterium_f_
^
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”), :
:1:373: unexpected input
1: s + Erythrobacter + Aeromicrobium + Renibacterium + Anaerosalibacter + Parvibaculum + Lachnospiraceae_NC2004_group + Finegoldia + Phascolarctobacterium + Ancylobacter + uncultured_bacterium_f
^
The tool produced the following additional output:
Number of significantly discriminative features: 25 ( 25 ) before internal Wilcoxon
How to solve this problem?