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

[C. Titus Brown]

Hi Diane, sorry, that's a bug in our code :(.

More in a bit -- 

best,
--titus

On Wed, Jun 03, 2015 at 04:40:36PM +0300, Diane Hatziioanou wrote:
>  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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-- 
C. Titus Brown, ctbrown at ucdavis.edu