I've generated a merged_abundance_table using output from MetaPhlAn2, merged using MetaPhlAn's "merge_metaphlan_tables.py" utility feature. When I plug this merged abundance table into LEfSe, I get an error at the run_lefse.py step:
Number of significantly discriminative features: 11 ( 11 ) before internal wilcoxon /home/linuxbrew/.linuxbrew/Cellar/lefse/1.0.0-dev-e3cabe9/libexec/lib/python2.7/site-packages/rpy2/robjects/functions.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 <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 "/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'
I'm uploading the merged table that seems to give the error when converted to .in and then used for the run_lefse.py step. If you can let me know what might be going wrong, it's greatly appreciated.