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lefse galaxy server #19

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dawnmy opened this issue May 12, 2022 · 0 comments
Open

lefse galaxy server #19

dawnmy opened this issue May 12, 2022 · 0 comments

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@dawnmy
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dawnmy commented May 12, 2022

Thank you for developing such useful tool. I used lefse galaxy service but gut the following 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"),  : 
  <text>:1:71: unexpected input
1: z <- suppressWarnings(lda(as.formula(class ~ Streptococcus_infantis + _
                                                                          ^

  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 <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 "/export/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/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 "/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"),  : 
  <text>:1:71: unexpected input
1: z <- suppressWarnings(lda(as.formula(class ~ Streptococcus_infantis + _
                                                                          ^

And I checked the taxa names there are no special chars. And the abundance values are in normal float value notation (not scientific notation). Could you help me out?

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