<div dir="ltr"><div><div>Thank you very much for the quick responses and tips, I'll battle that guide out tomorrow, another dumb question I have is is there any easy way to make a graph out of the histograms khmer makes to see if I have neat separate peaks of khmer distributions? Here is the sort of thing I'm looking for : <a href="http://ged.msu.edu/angus/_images/stamps-reads.png" target="_blank">http://ged.msu.edu/angus/_images/stamps-reads.png</a><br><br></div>Thanks in advance!<br></div>Diane<br><div><br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><pre cols="72">--
Dr Diane Hatziioanou
Greek Mobile: <a value="+306909403373">(+30)6909403373</a><br>UK Mobile: <a value="+447779516625">(+44)7779516625</a>
<a href="http://www.linkedin.com/in/dhatziioanou/" target="_blank">www.linkedin.com/in/dhatziioanou/</a>
<a href="https://twitter.com/DianeHIoanou" target="_blank">https://twitter.com/DianeHIoanou</a></pre></div></div></div>
<br><div class="gmail_quote">On 3 June 2015 at 16:50, C. Titus Brown <span dir="ltr"><<a href="mailto:ctbrown@ucdavis.edu" target="_blank">ctbrown@ucdavis.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Yes, but what I really wanted to do was point Diane at a somewhat more<br>
friendly set of instructions --<br>
<br>
so, here!<br>
<br>
<a href="https://khmer-protocols.readthedocs.org/en/latest/metagenomics/index.html" target="_blank">https://khmer-protocols.readthedocs.org/en/latest/metagenomics/index.html</a><br>
<br>
More soon...<br>
<br>
best,<br>
--titus<br>
<br>
On Wed, Jun 03, 2015 at 09:47:57AM -0400, Ramakrishnan Srinivasan wrote:<br>
> Titus,<br>
><br>
> Would adding a False to check_space() help?<br>
><br>
> --<br>
> Ram<br>
><br>
> On Wed, Jun 3, 2015 at 9:43 AM, C. Titus Brown <<a href="mailto:ctbrown@ucdavis.edu">ctbrown@ucdavis.edu</a>> wrote:<br>
><br>
> > Hi Diane, sorry, that's a bug in our code :(.<br>
> ><br>
> > More in a bit --<br>
> ><br>
> > best,<br>
> > --titus<br>
> ><br>
> > On Wed, Jun 03, 2015 at 04:40:36PM +0300, Diane Hatziioanou wrote:<br>
> > > Hello,<br>
> > ><br>
> > > I'm using khmer for the first time and have encountered a problem.<br>
> > > I'm running khmer version 1.4 and also using screed version 0.8.<br>
> > ><br>
> > > I have a dataset which is metagenomic-like with excessive coverage which<br>
> > I<br>
> > > have been following the basic metagenomic pipleline from the khmer page:<br>
> > ><br>
> > > 1. Apply single-pass digital normalization: normalize-by-median to<br>
> > C=20<br>
> > ><br>
> > > 2. Run filter-below-abund with C=100<br>
> > ><br>
> > > 1. Partition reads with load-graph, etc. etc.<br>
> > ><br>
> > > I did the load-graph.py, make-initial-stoptags.py and partition-graph.py<br>
> > > successfully following the guide at<br>
> > > <a href="http://khmer.readthedocs.org/en/latest/user/partitioning-big-data.html" target="_blank">http://khmer.readthedocs.org/en/latest/user/partitioning-big-data.html</a><br>
> > and<br>
> > > no matter what I do I can not make the find-knots.py work.<br>
> > ><br>
> > > The command I give is:<br>
> > ><br>
> > > find-knots.py -N 4 -x 8e9 C100Graph2 &<br>
> > ><br>
> > > I've also tried:<br>
> > ><br>
> > > find-knots.py C100Graph2 &<br>
> > ><br>
> > > and:<br>
> > ><br>
> > > find-knots.py C100Graph2 C100Graph2 &<br>
> > ><br>
> > > the message I always get is:<br>
> > ><br>
> > > Traceback (most recent call last):<br>
> > > File "/usr/local/bin/find-knots.py", line 154, in <module><br>
> > > main()<br>
> > > File "/usr/local/bin/find-knots.py", line 95, in main<br>
> > > check_space(infiles)<br>
> > > TypeError: check_space() takes at least 2 arguments (1 given)<br>
> > ><br>
> > > I can't find any help anywhere which described the two arguments needed,<br>
> > > all the examples i've seen only have one! Please let me know if you can<br>
> > see<br>
> > > what I'm doing wrongor if this is a known problem.<br>
> > ><br>
> > ><br>
> > > Yours sincerely,<br>
> > ><br>
> > > Artemis<br>
> > > --<br>
> > > Dr Diane Hatziioanou<br>
> > > Greek Mobile: (+30)6909403373<br>
> > > UK Mobile: (+44)7779516625<br>
> > > <a href="http://www.linkedin.com/in/dhatziioanou/" target="_blank">www.linkedin.com/in/dhatziioanou/</a><br>
> > > <a href="https://twitter.com/DianeHIoanou" target="_blank">https://twitter.com/DianeHIoanou</a><br>
> ><br>
> > > _______________________________________________<br>
> > > khmer mailing list<br>
> > > <a href="mailto:khmer@lists.idyll.org">khmer@lists.idyll.org</a><br>
> > > <a href="http://lists.idyll.org/listinfo/khmer" target="_blank">http://lists.idyll.org/listinfo/khmer</a><br>
> ><br>
> ><br>
> > --<br>
> > C. Titus Brown, <a href="mailto:ctbrown@ucdavis.edu">ctbrown@ucdavis.edu</a><br>
> ><br>
> > _______________________________________________<br>
> > khmer mailing list<br>
> > <a href="mailto:khmer@lists.idyll.org">khmer@lists.idyll.org</a><br>
> > <a href="http://lists.idyll.org/listinfo/khmer" target="_blank">http://lists.idyll.org/listinfo/khmer</a><br>
> ><br>
<span class="HOEnZb"><font color="#888888"><br>
--<br>
C. Titus Brown, <a href="mailto:ctbrown@ucdavis.edu">ctbrown@ucdavis.edu</a><br>
</font></span></blockquote></div><br></div>