Help with LEfSe second step

[Carlos Ruiz]

Hi everyone,

I'm having a problem when running LEfSe on the server, can you please help me out? The error the server shows is:

Traceback (most recent call last): File "/home/usr/local/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/394983afb1ee/lefse/run_lefse.py", line 4, in from lefse import * File "/home/usr/local/shed_tools/testtoolshed.g2.

Thanks!

[Zac Stephens]

Hi,

I am receiving the same error when trying to run LDA effect size.  If it is helpful, here's the full thing from "view report this error":

Traceback (most recent call last):
  File "/home/usr/local/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/394983afb1ee/lefse/run_lefse.py", line 4, in <module>
    from lefse import *
  File "/home/usr/local/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/394983afb1ee/lefse/lefse.py", line 3, in <module>
    import rpy2.robjects as robjects
  File "/usr/local/lib/python2.7/site-packages/rpy2/robjects/__init__.py", line 14, in <module>
    import rpy2.rinterface as rinterface
  File "/usr/local/lib/python2.7/site-packages/rpy2/rinterface/__init__.py", line 78, in <module>
    from rpy2.rinterface._rinterface import *
ImportError: /usr/local/lib/python2.7/site-packages/rpy2/rinterface/_rinterface.so: undefined symbol: Rf_PrintWarnings

Thanks,

Zac

[Nicola Segata]

Dear Zac and Carlos,

 thanks to George, this issue has been fixed. Please let us know if you encounter other issues.

many thanks

Nicola

[Diana Taft]

I suspect I am having a similar problem.  I get the following error message when running LEfSe, in multiple browsers and when using files that I have previously run successfully.

Thanks,

Diana

Traceback (most recent call last):
  File "/home/usr/local/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/394983afb1ee/lefse/run_lefse.py", line 4, in <module>
    from lefse import *
  File "/home/usr/local/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/394983afb1ee/lefse/lefse.py

", line 3, in <module>
    import rpy2.robjects as robjects
  File "/usr/local/lib/python2.7/site-packages/rpy2/robjects/__init__.py", line 18, in <module>
    from rpy2.robjects.robject import RObjectMixin, RObject
  File "/usr/local/lib/python2.7/site-packages/rpy2/robjects/robject.py", line 9, in <module>
    class RObjectMixin(object):
  File "/usr/local/lib/python2.7/site-packages/rpy2/robjects/robject.py", line 22, in RObjectMixin
    __show = rpy2.rinterface.baseenv.get("show")
LookupError: 'show' not found

The tool produces the following additional output:

Error : object 'anyNA' not found whilst loading namespace 'grDevices'
In addition: Warning messages:
1: FALSE 
2: FALSE 
3: FALSE 
4: FALSE 
5: FALSE 
6: FALSE 
7: FALSE 
Error : object 'anyNA' not found whilst loading namespace 'grDevices'
In addition: Warning messages:
1: FALSE 
2: FALSE 
Error : object 'anyNA' not found whilst loading namespace 'grDevices'
In addition: Warning messages:
1: FALSE 
2: FALSE 
During startup - Warning messages:
1: FALSE 
2: FALSE 
3: FALSE 

[Gary Lecleir]

I am experiencing the same issues as Diana.  I am getting errors with multiple browsers on files that I've used previously.  

Many Thanks, 

Gary

[Caitlin Ryan]

I've been having similar issues with lefse for the past few days on galaxy and from my own computer. First issue, galaxy version would run an error trying to format data that I had previously successfully formatted. I have yet to get my local version of lefse to format any data set. (Recently, it seems like I can format on galaxy again, but not locally).  I notice now if you drop the subclass from the data, you can successfully format the data and run an LDA (in galaxy, only). 

Errors for formatting from my computer running python format_input.py:

Traceback (most recent call last):

  File "format_input.py", line 413, in <module>

    params['subject']-1 if not params['subject'] is None else None))

  File "format_input.py", line 117, in sort_by_cl

    if n == 3: data.sort(sort_lines3)                                                                                  

  File "format_input.py", line 115, in sort_lines3

    if a[s] != b[s]: return int(a[s] > b[s])*2-1                                                                          

IndexError: tuple index out of range

When trying to run the LDA on my data in galaxy I get the following:

Traceback (most recent call last):
  File "/home/usr/local/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/394983afb1ee/lefse/run_lefse.py", line 67, in <module>
    kw_ok,pv = test_kw_r(cls,feat_values,params['anova_alpha'],sorted(cls.keys()))
  File "/home/usr/local/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/394983afb1ee/lefse/lefse.py", line 60, in test_kw_r
    kw_res = robjects.r('kruskal.test('+fo+',)$p.value')
  File "/usr/local/lib/python2.7/site-packages/rpy2/robjects/__init__.py", line 240, in __call__
    res = self.eval(p)
  File "/usr/local/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 86, in __call__
    return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
  File "/usr/local/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 35, in __call__
    res = super(Function, self).__call__(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error in kruskal.test.formula(y ~ x1 + x2, ) : 
  'formula' should be of the form response ~ group

And I have yet to get my local version of lefse to run... even with formatted .lefse files from galaxy. I've installed all dependancies, every version is updated etc, etc.

Anybody have an idea how to fix?

Cait

[Diana Taft]

Well, the good news is that today I am able to run the second step of LEfSe.  I am now having trouble with plotting the results - I select pdf, but instead I get png output.  Is anyone else having this problem as well?

Thanks

Diana

[George Weingart]

Hello everyone,

The problems in the second step of Lefse  were related to a Galaxy upgrade we performed.

They  were solved Friday.

Please let me know if you encounter them again.

The problem consisted of the fact that Galaxy required an upgrade to R 3.1 and an upgrade to rpy2.

Best regards,

George

[Christopher Anderson]

I am still getting the error posted below when calculating the LDA Effect Size from a formatted file.  This is a different error than a few days ago, but this is still from a sample file that worked previously.

Traceback (most recent call last):
  File "/home/usr/local/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/394983afb1ee/lefse/run_lefse.py", line 67, in <module>
    kw_ok,pv = test_kw_r(cls,feat_values,params['anova_alpha'],sorted(cls.keys()))
  File "/home/usr/local/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/394983afb1ee/lefse/lefse.py", line 60, in test_kw_r
    kw_res = robjects.r('kruskal.test('+fo+',)$p.value')
  File "/usr/local/lib/python2.7/site-packages/rpy2/robjects/__init__.py", line 240, in __call__
    res = self.eval(p)
  File "/usr/local/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 86, in __call__
    return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
  File "/usr/local/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 35, in __call__
    res = super(Function, self).__call__(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error in kruskal.test.formula(y ~ x1 + x3, ) : 
  'formula' should be of the form response ~ group

[Gary LeCleir]

I still am getting an error as well.  I seem to only be having this issue when I attempt to run lefse with subclasses.

Traceback (most recent call last):
  File "/home/usr/local/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/394983afb1ee/lefse/run_lefse.py", line 67, in <module>
    kw_ok,pv = test_kw_r(cls,feat_values,params['anova_alpha'],sorted(cls.keys()))
  File "/home/usr/local/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/394983afb1ee/lefse/lefse.py

", line 60, in test_kw_r
    kw_res = robjects.r('kruskal.test('+fo+',)$p.value')
  File "/usr/local/lib/python2.7/site-packages/rpy2/robjects/__init__.py", line 240, in __call__
    res = self.eval(p)
  File "/usr/local/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 86, in __call__
    return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
  File "/usr/local/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 35, in __call__
    res = super(Function, self).__call__(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error in kruskal.test.formula(y ~ x1 + x2 + x3, ) : 
  'formula' should be of the form response ~ group

Thanks,

Gary

--
Gary LeCleir
University of Tennessee
Department of Microbiology

[Caitlin Ryan]

Bingo! Me too.