[khmer] Digital normalization

C. Titus Brown ctb at msu.edu
Mon Aug 26 10:27:05 PDT 2013


Hi Joann,

could you send us the output of

gunzip -c *.se.qc.fq.gz | head

pls? thanks! I wonder what's in that file if it's not FQ?

--titus

On Mon, Aug 26, 2013 at 10:15:05AM -0600, Joann Diray Arce wrote:
> 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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> khmer at lists.idyll.org
> http://lists.idyll.org/listinfo/khmer


-- 
C. Titus Brown, ctb at msu.edu




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