[khmer] Iowa corn run test

Ramakrishnan Srinivasan ramrs at nyu.edu
Wed Apr 23 06:17:48 PDT 2014


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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