[khmer] Digital normalization

Joann Diray Arce joann.diray at gmail.com
Mon Aug 26 09:15:05 PDT 2013

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):
line 156, in <module>
line 85, in main
    for n, batch in enumerate(batchwise(screed.open(input_filename),
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
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