# Error in run\_lefse.py
**URL:** https://forum.biobakery.org/t/error-in-run-lefse-py/5190
**Category:** LEfSe
**Created:** [April 24, 2023, 1:53am UTC](https://forum.biobakery.org/t/error-in-run-lefse-py/5190 "2023-04-24T01:53:34Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@hchen815](https://forum.biobakery.org/u/hchen815)
#### Post date: [April 24, 2023, 1:53am UTC](https://forum.biobakery.org/t/error-in-run-lefse-py/5190/1 "2023-04-24T01:53:34Z")
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 ?
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### Author:  [@andrewGhazi](https://forum.biobakery.org/u/andrewGhazi)
#### Post date: [April 24, 2023, 3:30pm UTC](https://forum.biobakery.org/t/error-in-run-lefse-py/5190/2 "2023-04-24T15:30:37Z")
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.