LEfSe Formatting Error

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I am attempting to run LEfSe on metagenomic data from the microbiome. We have used the same classification database many times without issue, but now I am receiving the error below. All spaces and other potentially problematic characters have been removed. It crashes during the “LDA Effect Size” step. Any guidance would be much appreciated.

/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 ~ Flavonifractor_plautii +                                                                 ^

  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 ~ Flavonifractor_plautii + _
                                                                          ^

admin reformat

1 Like
2

Welcome, @rbrewster!

This does look like an input formatting problem and not a tool problem.

Choices:

  • You could confirm that the tool itself (including dependencies) is actually intact by rerunning the tool with data that previously ran through the tool successfully to see what happens.

  • If that works, then try comparing your prior data input formats to the new data inputs. Headers, data lines, etc.

  • If that doesn’t work for some reason, you might want to consider updating to a newer version of the tool. Galaxy has been updated since this tool was, there might be some incompatibility. The version you are using is from the Test ToolShed – and tools from this source are generally not recommended. There is a (presumably stable) version from this same community developer in the Main ToolShed https://usegalaxy.org (warning: also several years old, so consider this carefully and test).

  • If that new version from the MTS also presents problems, you could contact the tool wrapper author through the ToolShed (log in and see “Repository Actions”). They did not link in a development repository, so you can’t open/review tickets/known issues there, unfortunately.

  • The IUC also has a recently updated version (inputs are reformatted Mothur outputs, if that would work for you). You’ll want to use the complete updated Mothur tool suite from the IUC if you decide to go this route – there were many updates in the last revision. Trying to combine older/newer tools and data will be problematic for several steps (that I’ve noticed).