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timiat

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Jul 23rd, 2014
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  1. hlw@skarrow:~/khmer/scripts/ $ python normalize-by-median.py -f -k 17 -x 1 ../tests/test-data/test-fastq-reads.fq
  2.  
  3. || This is the script 'normalize-by-median.py' in khmer.
  4. || You are running khmer version 1.1-117-g2482a3e
  5. || You are also using screed version 0.7
  6. ||
  7. || If you use this script in a publication, please cite EACH of the following:
  8. ||
  9. || * MR Crusoe et al., 2014. doi: 10.6084/m9.figshare.979190
  10. || * CT Brown et al., arXiv:1203.4802 [q-bio.GN]
  11. ||
  12. || Please see the CITATION file for details.
  13.  
  14.  
  15. PARAMETERS:
  16. - kmer size = 17 (-k)
  17. - n tables = 4 (-N)
  18. - min tablesize = 1 (-x)
  19.  
  20. Estimated memory usage is 4 bytes (n_tables x min_tablesize)
  21. --------
  22. making k-mer counting table
  23. DONE with ../tests/test-data/test-fastq-reads.fq; kept 6 of 100 or 6%
  24. output in test-fastq-reads.fq.keep
  25. fp rate estimated to be 1.000
  26. **
  27. ** ERROR: the k-mer counting table is too small for this data set. Increase tablesize/# tables.
  28. **
  29. ** Do not use these results!!
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