[khmer] Using khmer for producing k-mer frequency distribution

C. Titus Brown ctb at msu.edu
Wed Aug 28 07:38:25 PDT 2013


On Wed, Aug 28, 2013 at 10:36:31AM -0400, Rajat Shuvro Roy wrote:
> Thanks. I fixed the python path problem and it is now invoking khmer from
> the new location.
> 
> python -c "import khmer; print khmer"
> <module 'khmer' from '/home/rajatroy/khmer/python/khmer/__init__.pyc'>
> 
> I tried to invoke the default mode with :
> 
> python load-into-counting.py  -k 31  out.kh 1Mreads.fa
> 
> But it probably is not invoking the default mode where the memory should be
> expanding indefinitely. It says:
> 
> PARAMETERS:
>  - kmer size =    31            (-k)
>  - n hashes =     4             (-N)
>  - min hashsize = 1e+06         (-x)
> 
> Estimated memory usage is 4e+06 bytes (n_hashes x min_hashsize)
> --------
> ** WARNING: hashsize is default!  You absodefly want to increase this!
> ** Please read the docs!

Hi Rajat, you still need to set the basic memory usage:

https://khmer.readthedocs.org/en/latest/choosing-hash-sizes.html

cheers,
--titus




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