[khmer] Digital normalization

[Joann Diray Arce]

I actually ran this last week. Do I need to reinstall khmer? OR should I
start from my original fastq and see how it goes.


Estimated memory usage is 1.2e+10 bytes (n_hashes x min_hashsize)
--------
Traceback (most recent call last):
  File
"/fslhome/jdiray/compute/SuaedaIllumina2013/khmer/scripts/normalize-by-median.py",
line 156, in <module>
    main()
  File
"/fslhome/jdiray/compute/SuaedaIllumina2013/khmer/scripts/normalize-by-median.py",
line 85, in main
    for n, batch in enumerate(batchwise(screed.open(input_filename),
batch_size)):
  File
"/fslhome/jdiray/compute/SuaedaIllumina2013/lib/python2.7/site-packages/screed/fastq.py",
line 21, in fastq_iter
    raise IOError("Bad FASTQ format: no '@' at beginning of line")
IOError: Bad FASTQ format: no '@' at beginning of line

My output files end usually at 9%

Here is my code:
python /..../khmer/scripts/normalize-by-median.py -k 20 -C 20 -N 4 -x 3e9
--loadhash normC20k20.kh --savehash normC20k20.kh *.se.qc.fq.gz

-- 
*Joann Diray Arce*
Graduate Student
Department of Microbiology and Molecular Biology
Brigham Young University
(801)7352371
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