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

Ramakrishnan Srinivasan ramrs at nyu.edu
Wed Jun 3 06:47:57 PDT 2015


Titus,

Would adding a False to check_space() help?

--
Ram

On Wed, Jun 3, 2015 at 9:43 AM, C. Titus Brown <ctbrown at ucdavis.edu> wrote:

> 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
>
> > _______________________________________________
> > khmer mailing list
> > khmer at lists.idyll.org
> > http://lists.idyll.org/listinfo/khmer
>
>
> --
> C. Titus Brown, ctbrown at ucdavis.edu
>
> _______________________________________________
> khmer mailing list
> khmer at lists.idyll.org
> http://lists.idyll.org/listinfo/khmer
>
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