Error in run_lefse.py

Downstream analysis and statistics LEfSe
1

Im using LEfse 1.0 in Linux-ubantu. I also put the lefse in singularity, when I run the code : singularity exec ~/software/software/lefse_latest.sif run_lefse.py S_S_BF.lefse.in S_S_BF.lefse.out.
I got the error messgae:
.py:106: UserWarning: Error in svd(X, nu = 0L) : infinite or missing values in ‘x’

res = super(Function, self).call(*new_args, **new_kwargs)
Traceback (most recent call last):
File “/home/linuxbrew/.linuxbrew/Cellar/lefse/1.0.0-dev-e3cabe9/libexec/bin/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 “/home/linuxbrew/.linuxbrew/Cellar/lefse/1.0.0-dev-e3cabe9/libexec/bin/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 “/home/linuxbrew/.linuxbrew/Cellar/lefse/1.0.0-dev-e3cabe9/libexec/lib/python2.7/site-packages/rpy2/robjects/init.py”, line 321, in call
res = self.eval(p)
File “/home/linuxbrew/.linuxbrew/Cellar/lefse/1.0.0-dev-e3cabe9/libexec/lib/python2.7/site-packages/rpy2/robjects/functions.py”, line 178, in call
return super(SignatureTranslatedFunction, self).call(*args, **kwargs)
File “/home/linuxbrew/.linuxbrew/Cellar/lefse/1.0.0-dev-e3cabe9/libexec/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’

May I know how to fixed the problem ?

2

The error message states that you have either infinite or missing values in your input, so that’s your core problem. Double check your input for that. It may also help for you to run the example to confirm that it works, then compare your input to the example input, just to make sure things are formatted correctly.