Hi,
i have installed lefse with conda and have been facing error message when i run lefse_run.py. Not sure what is going wrong. I cannot seem to access lefse on Galaxy too. I’ll attach my input file here.
BS-anvio-family-lefse.txt (228.7 KB)
Any help will be appreciated.
Error:
Number of significantly discriminative features: 293 ( 293 ) before internal wilcoxon
R[write to console]: Error in terms.formula(formula, data = data) :
invalid model formula in ExtractVars
R[write to console]: In addition:
R[write to console]: Warning messages:
R[write to console]: 1: package ‘mvtnorm’ was built under R version 4.1.3
R[write to console]: 2: package ‘modeltools’ was built under R version 4.1.3
R[write to console]: 3: package ‘coin’ was built under R version 4.1.3
Traceback (most recent call last):
File "/home/combio7/anaconda3/bin/lefse_run.py", line 10, in <module>
sys.exit(lefse_run())
File "/home/combio7/anaconda3/lib/python3.8/site-packages/lefse/lefse_run.py", line 90, in lefse_run
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 "/home/combio7/anaconda3/lib/python3.8/site-packages/lefse/lefse.py", line 206, in test_lda_r
z = robjects.r('z <- suppressWarnings(lda(as.formula('+f+'),data=sub_d,tol='+str(tol_min)+'))')
File "/home/combio7/anaconda3/lib/python3.8/site-packages/rpy2/robjects/__init__.py", line 459, in __call__
res = self.eval(p)
File "/home/combio7/anaconda3/lib/python3.8/site-packages/rpy2/robjects/functions.py", line 207, in __call__
return (super(SignatureTranslatedFunction, self)
File "/home/combio7/anaconda3/lib/python3.8/site-packages/rpy2/robjects/functions.py", line 130, in __call__
res = super(Function, self).__call__(*new_args, **new_kwargs)
File "/home/combio7/anaconda3/lib/python3.8/site-packages/rpy2/rinterface_lib/conversion.py", line 45, in _
cdata = function(*args, **kwargs)
File "/home/combio7/anaconda3/lib/python3.8/site-packages/rpy2/rinterface.py", line 817, in __call__
raise embedded.RRuntimeError(_rinterface._geterrmessage())
rpy2.rinterface_lib.embedded.RRuntimeError: Error in terms.formula(formula, data = data) :
invalid model formula in ExtractVars