Error in Step B LDA Effect Size (LEfSe)


I’m trying to proceed to step B. After searching around, I did found someone else having similar issue. The following error was received:

/galaxy_venv/local/lib/python2.7/site-packages/rpy2/rinterface/ RRuntimeWarning: Error in La.svd(x, nu, nv) : error code 1 from Lapack routine ‘dgesdd’

warnings.warn(x, RRuntimeWarning)
Traceback (most recent call last):
File “/shed_tools/”, 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/”, 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/”, line 359, in call
res = self.eval(p)
File “/galaxy_venv/local/lib/python2.7/site-packages/rpy2/robjects/”, line 178, in call
return super(SignatureTranslatedFunction, self).call(*args, **kwargs)
File “/galaxy_venv/local/lib/python2.7/site-packages/rpy2/robjects/”, line 106, in call
res = super(Function, self).call(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error in La.svd(x, nu, nv) : error code 1 from Lapack routine ‘dgesdd’

Attached is the data I use.
bf_ptmid_lefse_nosqrt campy.txt (762.5 KB)

Appreciate any help and input.


Hello Xinran,
LEfSe will often have errors if special characters are used in labels, such as “+” or “-” like you have in your data. I recommend replacing those labels with alphanumeric ones (“positive” and “negative” for instance) and trying to re-run.

Hi Meg,

Thank you for helping. I tried as you suggested, but I still had the error. Then I figured that the format of cells containing relative abundance data in excel should be all scientific. Where in my data I have some cells in scientific format and others in regular format. Once I uniformed the style, the error seems to be solved.


Good to hear, and thank you for sharing what fixed the problem!