[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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