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

[C. Titus Brown]

Yes, but what I really wanted to do was point Diane at a somewhat more
friendly set of instructions --

so, here!

https://khmer-protocols.readthedocs.org/en/latest/metagenomics/index.html

More soon...

best,
--titus

On Wed, Jun 03, 2015 at 09:47:57AM -0400, Ramakrishnan Srinivasan wrote:
> 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
> >

-- 
C. Titus Brown, ctbrown at ucdavis.edu