[khmer] Khmer troubleshooting

Michael R. Crusoe mcrusoe at msu.edu
Mon Mar 3 15:09:18 PST 2014


Hello,

Which tutorial are you using?

If you are following the khmer-protocols then place to ask for help is
https://github.com/ged-lab/khmer-protocols/issues?state=open


On Mon, Mar 3, 2014 at 3:31 PM, Shu CHEN <szc0049 at tigermail.auburn.edu>wrote:

>   Hi,
>
>
>  I followed your tutorial of using Khmer in the amzon EC2. After I ran
> the 'make test', it gave me a error feed back as:
>
> tests.test_scripts.test_normalize_by_median_version ... ERROR
>
> ======================================================================
> ERROR: tests.test_scripts.test_normalize_by_median_version
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/lib/pymodules/python2.7/nose/case.py", line 187, in runTest
>     self.test(*self.arg)
>   File "/home/ubuntu/khmer/tests/test_scripts.py", line 392, in
> test_normalize_by_median_version
>     status, out, err = popenscript(script, args)
>   File "/home/ubuntu/khmer/tests/test_scripts.py", line 135, in popenscript
>     raise Exception(status, out, err)
> Exception: (1, '', 'Traceback (most recent call last):\n  File
> "/home/ubuntu/khmer/scripts/normalize-by-median.py", line 19, in
> <module>\n    import khmer\nImportError: No module named khmer\n')
> -------------------- >> begin captured stdout << ---------------------
> running: /home/ubuntu/khmer/scripts/normalize-by-median.py in: None
> arguments ['--version']
>
> Can you help me fix this issue?
>
>
>   Shu Chen
>
> Ph.D. Student
>
> Department of Agronomy and Soils
>
> RM 165, Funchess Hall
>



-- 
Michael R. Crusoe:  Programmer & Bioinformatician   mcrusoe at msu.edu
 @ the Genomics, Evolution, and Development lab; Michigan State U
http://ged.msu.edu/ http://orcid.org/0000-0002-2961-9670
@biocrusoe<http://twitter.com/biocrusoe>
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