<div dir="ltr">Thanks so much. I downloaded and compiled the latest version. make test resulted in 'ok' for everything. However, when I tried to run it, I get the following message:<div><br></div><div><div>python load-into-counting.py -k 31 -x 5e10 <a href="http://out.kh">out.kh</a> 1Mreads.fa </div>
<div>Traceback (most recent call last):</div><div> File "load-into-counting.py", line 13, in <module></div><div> from khmer.counting_args import build_construct_args, report_on_config</div><div>ImportError: cannot import name report_on_config</div>
</div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Aug 27, 2013 at 4:41 PM, C. Titus Brown <span dir="ltr"><<a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Rajat,<br>
<br>
sorry for long delay in response!<br>
<div class="im"><br>
On Thu, Jul 18, 2013 at 03:32:39PM -0400, Rajat Shuvro Roy wrote:<br>
</div><div><div class="h5">> Hello Prof Brown,<br>
> I was attempting to produce a k-mer frequency distribution using khmer and<br>
> followed the instructions in (<br>
> <a href="http://khmer.readthedocs.org/en/latest/scripts.html" target="_blank">http://khmer.readthedocs.org/en/latest/scripts.html</a>) . I have a Zia mays<br>
> library (SRR404240, 95.8Gbp ) and I executed the following command.<br>
><br>
> python load-into-counting.py -k 31 -x 5e10 <a href="http://out.kh" target="_blank">out.kh</a> SRR404240.fasta<br>
><br>
> I believe, this counts k-mer frequencies and the script abundance-dist.py<br>
> produces the distribution.<br>
><br>
> We stopped it after it had ran for 2464 mins (41hrs) using 187GB space. I<br>
> tried with smaller values for -x but failed to complete the computation in<br>
> less than 3 days. Could you please let us know if this is expected and we<br>
> should allow more time. And is there a more efficient way of using Khmer?<br>
<br>
</div></div>Your e-mail actually triggered some doc changes and updates ;).<br>
<br>
Briefly, khmer can count k-mers in either constant-memory mode or in<br>
accurate-large-counts mode. In the former, counts above 255 will<br>
stop being counted, but the memory specified with the -N and -x parameters<br>
will be the total amount used; in the latter mode (which is the default),<br>
counts above 255 will be kept and memory use will expand indefinitely.<br>
<br>
You can use these modes easily in the latest khmer, the bleeding-edge<br>
branch; you can get that like so:<br>
<br>
git clone <a href="https://github.com/ged-lab/khmer.git" target="_blank">https://github.com/ged-lab/khmer.git</a> -b bleeding-edge<br>
<br>
Then use 'load-into-counting.py -b' to build the tables, and 'abundance-dist'<br>
to generate the output.<br>
<br>
I'd suggest running it on a small test data set (data/25k.fq.gz, in the<br>
khmer repo) just to make sure it all works for you, but it should - we use<br>
this regularly.<br>
<br>
Please let me know if you have any questions, and again, apologies for<br>
the delay!<br>
<br>
cheers,<br>
--titus<br>
<div class="HOEnZb"><div class="h5">--<br>
C. Titus Brown, <a href="mailto:ctb@msu.edu">ctb@msu.edu</a><br>
</div></div></blockquote></div><br></div>