[khmer] cannot run the latest version of normalize-by-median.py

cy_jiang cy_jiang at 126.com
Tue Aug 27 17:03:57 PDT 2013

Hi Titus,

I have downloaded the latest version of khmer and tried to run the normalize-by-median.py (command line:/khmer/scripts/normalize-by-median.py -k 20 -C 20 -x 7.5e9 -N 4 --savehash mh.kh T_allR1R2.py), but it prompted up with the following information:

Traceback (most recent call last):
  File "/home/work/khmer/scripts/normalize-by-median.py", line 241, in <module>
  File "/home/work/khmer/scripts/normalize-by-median.py", line 140, in main
    ' - kmer size =    {:d} \t\t(-k)'.format(args.ksize)
ValueError: zero length field name in format

This command line ran pretty well with the older version of khmer. Can you give me a clue what is going on there?

Besides, I wonder how to choose a better k-mer size. As I am going to assemble my dataset with Trinity, I am thinking would it be better using a k-mer value of 25 since Trinity set this default k-mer size when it does the assembly. 

Hope to hear from you soon and thanks in advance!

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