[khmer] Iowa corn run test
C. Titus Brown
ctb at msu.edu
Wed Apr 23 19:15:59 PDT 2014
On Wed, Apr 23, 2014 at 09:17:48AM -0400, Ramakrishnan Srinivasan wrote:
> This bug has now been fixed in the master branch of khmer. Thanks to
> @chuckpr and Emeric for finding the bug and testing the fix.
> On Wed, Apr 16, 2014 at 9:44 AM, Ramakrishnan Srinivasan <ramrs at nyu.edu>wrote:
> > Hello Emeric,
> > Thank you for the email. I just checked the code, and there seems to be a
> > tiny bug. It should be fixed within the day, and I shall send an update
> > once the patch is done.
> > Thank you for identifying the bug!
> > If you would like to correct it on your local copy, you might try
> > changing the '.ht' in Line #74, Col 28 of scripts/make-initial-stoptags.py
> > to '.pt' so it looks like this:
> > infiles = [graphbase + '.pt', graphbase + '.tagset']
> > --
> > Ram
> > On Wed, Apr 16, 2014 at 8:55 AM, Emeric Sevin <emeric.sevin at u-bordeaux.fr>wrote:
> >> Hi all,
> >> Not sure this is the designated list for my question, but I just can't
> >> seem to find a better destination contact.
> >> My problem will likely be pretty low-profile, but I've tried to run the
> >> Iowa Corn test case you provided (https://khmer.readthedocs.
> >> org/en/latest/partitioning-big-data.html), and I'm confronted with a
> >> frustrating setback. Basically everything works fine during the first
> >> partition step, but when I try to break up the lump in the 2nd pass,
> >> make-initial-stoptags.py keeps exiting with this message:
> >> ERROR: Input file lump.ht does not exist; exiting
> >> Indeed, no lump.ht file is created by load-graph.py, and I can't find
> >> any option or trigger which would allow me to correct that...
> >> even though I've been following your cookbook almost to the letter
> >> (except memory-wise)....
> >> Thanks in advance for your answer,
> >> Best regards
> >> Emeric
> >> _______________________________________________
> >> khmer mailing list
> >> khmer at lists.idyll.org
> >> http://lists.idyll.org/listinfo/khmer
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> khmer at lists.idyll.org
C. Titus Brown, ctb at msu.edu
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