[khmer] find-knots.py error: what are the 2 arguments?

[Diane Hatziioanou]

 Hello,

I'm using khmer for the first time and have encountered a problem.
I'm running khmer version 1.4 and also using screed version 0.8.

I have a dataset which is metagenomic-like with excessive coverage which I
have been following the basic metagenomic pipleline from the khmer page:

   1. Apply single-pass digital normalization: normalize-by-median to C=20

      2. Run filter-below-abund with C=100

   1. Partition reads with load-graph, etc. etc.

I did the load-graph.py, make-initial-stoptags.py and partition-graph.py
successfully following the guide at
http://khmer.readthedocs.org/en/latest/user/partitioning-big-data.html and
no matter what I do I can not make the find-knots.py work.

The command I give is:

find-knots.py -N 4 -x 8e9 C100Graph2 &

I've also tried:

find-knots.py C100Graph2 &

and:

find-knots.py C100Graph2 C100Graph2 &

the message I always get is:

Traceback (most recent call last):
  File "/usr/local/bin/find-knots.py", line 154, in <module>
    main()
  File "/usr/local/bin/find-knots.py", line 95, in main
    check_space(infiles)
TypeError: check_space() takes at least 2 arguments (1 given)

I can't find any help anywhere which described the two arguments needed,
all the examples i've seen only have one! Please let me know if you can see
what I'm doing wrongor if this is a known problem.


Yours sincerely,

Artemis
--
Dr Diane Hatziioanou
Greek Mobile: (+30)6909403373
UK Mobile: (+44)7779516625
www.linkedin.com/in/dhatziioanou/
https://twitter.com/DianeHIoanou
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