[khmer] kmer counting stops at 248

[C. Titus Brown]

On Sun, Jul 27, 2014 at 01:32:43PM +0300, Alon philosof wrote:
> Hello,
> i?ve came across a strange behaviour:
> I?ve installed Khmer 1.1 on a server running torque, since I don?t have root privileges I?ve downloaded the source and installed by: python setup.py install ?user.
> things seems to be working OK and I have attempted to count kmers and calculate histogram on a ~10gb metagenome file with:
> 
> .local/bin/load-into-counting.py --ksize 21 --threads 8 --min-tablesize 250e9 --n_tables 4 out.kh in.fastq
> 
> .local/bin/abundance-dist.py out.kh in.fastq out.hist
> 
> the resulting histogram shows counts up to only 248. I am running this with enough memory allocated and load-into-counting runs to completion without raising errors.
> in addition, I?d like to note that it runs on a single machine and not on multiple nodes.
> 
> however, when I run load-into-counting (--min-tablesize 64e8 --n_tables 4) on my local Ubuntu machine (32gb of ram)  running the same khmer 1.1 build  It runs to completion and calculates all kmers in the file.
> 
> when I abundance-dist.py on a .kh file from the server it again show counts to 248 only.
> 
> have you came across this behaviour before? any ideas how to solve that?

Hi Alon,

How strange -- nothing comes to mind immediately, I must admit :).

What happens when you run the tests? If you're in a virtualenv 'make test'
should work; if not, we have fixed a few problems in the latest master branch,
and you could run through our "getting started with development" docs

http://khmer.readthedocs.org/en/docs-hackathon/dev/getting-started.html

to use the latest branch.

My first guess is that one of the two machines is compiling in 32-bit mode.
If so, the tests will show that.

Thanks for any feedback you can give! This sort of thing worries me because
it hints at bigger potential problems :)

best,
--titus
-- 
C. Titus Brown, ctb at msu.edu