LDA Lefse error : 2nd step

Downstream analysis and statistics LEfSe
1

Hello,

Is there anyone who encountered this same error:

/galaxy_venv/local/lib/python2.7/site-packages/rpy2/rinterface/init.py:185: RRuntimeWarning: Error in (function (file = “”, n = NULL, text = NULL, prompt = “?”, keep.source = getOption(“keep.source”), :
:1:47: unexpected symbol
1: effect.size ← abs(mean(LD[sub_d[,“class”]==""Patient
^

warnings.warn(x, RRuntimeWarning)
Traceback (most recent call last):
File “/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/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 “/export/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/lefse.py”, line 199, in test_lda_r
robjects.r(‘effect.size ← abs(mean(LD[sub_d[,“class”]=="’+p[0]+‘“]) - mean(LD[sub_d[,“class”]==”’+p[1]+‘"]))’)
File “/galaxy_venv/local/lib/python2.7/site-packages/rpy2/robjects/init.py”, line 358, in call
p = _rparse(text=StrSexpVector((string,)))
rpy2.rinterface.RRuntimeError: Error in (function (file = “”, n = NULL, text = NULL, prompt = “?”, keep.source = getOption(“keep.source”), :
:1:47: unexpected symbol
1: effect.size ← abs(mean(LD[sub_d[,“class”]==""Patient

I’ve tried reformatting my input files based on the suggestions in the forum but still it doesnt work.

Here’s a header of my data:

“Group” “Healthy” “Healthy” “Healthy” “Healthy” “Healthy” “Patient” “Patient” “Patient” “Patient” “Patient”
“Samples” “HSO” “NYJ” “LJH” “YHY” “LCH” “KSH” “KHK” “HMG” “GYJ” “CYY”
“Bacteria|Actinobacteria|Actinobacteria|Corynebacteriales|Corynebacteriaceae|Corynebacterium 1|2.0” 8.96949474836083E-06 0.005553861255921 0 8.17833681253412E-05 9.38594512350751E-05 4.12102630038985E-05 2.34245250091941E-06 0.000298544595099 0.008180762510446 0.012217649534677
“Bacteria|Actinobacteria|Actinobacteria|Corynebacteriales|Corynebacteriaceae|Corynebacterium 1|uncultured bacterium” 0.00019284413709 0.008398696236431 1.10870890847608E-06 0.000139031725813 0.000302984895215 0.000138054381063 0 0.001027135571233 0.025877169182684 0.043901697610251
“Bacteria|Firmicutes|Bacilli|Bacillales|Staphylococcaceae|Staphylococcus|44.0” 0.000197328884464 6.43304392577697E-05 0 0 6.91595956468975E-05 8.2420526007797E-05 0.00073787253779 0 0.001653950924107 0.000526118879484
“Bacteria|Actinobacteria|Actinobacteria|Corynebacteriales|Corynebacteriaceae|Corynebacterium 1|Corynebacterium segmentosum” 0 0 0 0 0 0 0 0 0 1.16915306551934E-05

I need some advise.
Thank you

Best,
James

2

Hi,
Are you running LEfSe on Galaxy or locally? If locally, can you send me the version number and the line of code you ran to get this error?
Thanks,
Meg

3

Hello Meg,

Thanks for your response. I did the analysis on Galaxy Lefse. Step 1 (Format Data for Lefse) was working fine. However, when I use it for Step 2 (LDA effect size) it makes that error saying:

Number of significantly discriminative features: 5 ( 5 ) before internal wilcoxon
/galaxy_venv/local/lib/python2.7/site-packages/rpy2/rinterface/init.py:185: RRuntimeWarning: Error in (function (file = “”, n = NULL, text = NULL, prompt = “?”, keep.so

How should I proceed?

Thanks
James