Run properly in the galaxy but raise an error in the bioconda lefse

Downstream analysis and statistics LEfSe
1

Thanks for your attention.

For my test data, lefse analysis was run properly in the galaxy. But raise an error while lefse analysis is performed using the bioconda lefse. The error is similarity to this one.

summarized_abd.txt (24.5 KB)

/miniconda3/envs/lefse/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:186: RRuntimeWarning: Error in svd(X, nu = 0L) : infinite or missing values in 'x'

  warnings.warn(x, RRuntimeWarning)
Traceback (most recent call last):
  File "/Users/caoyang/miniconda3/envs/lefse/bin/run_lefse.py", line 90, in <module>
    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 "/Users/caoyang/miniconda3/envs/lefse/bin/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 "/Users/caoyang/miniconda3/envs/lefse/lib/python2.7/site-packages/rpy2/robjects/__init__.py", line 363, in __call__
    res = self.eval(p)
  File "/Users/caoyang/miniconda3/envs/lefse/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 178, in __call__
    return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
  File "/Users/caoyang/miniconda3/envs/lefse/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 106, in __call__
    res = super(Function, self).__call__(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error in svd(X, nu = 0L) : infinite or missing values in 'x'