<div dir="ltr"><div class="gmail_default" style="font-family:trebuchet ms,sans-serif">Titus,</div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif"><br></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif">Would adding a False to check_space() help?</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr">--<br><div><font face="garamond, serif">Ram</font></div></div></div></div>
<br><div class="gmail_quote">On Wed, Jun 3, 2015 at 9:43 AM, 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">Hi Diane, sorry, that's a bug in our code :(.<br>
<br>
More in a bit --<br>
<br>
best,<br>
--titus<br>
<span class=""><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 I<br>
> have been following the basic metagenomic pipleline from the khmer page:<br>
><br>
</span>> 1. Apply single-pass digital normalization: normalize-by-median to C=20<br>
<span class="">><br>
> 2. Run filter-below-abund with C=100<br>
><br>
</span>> 1. Partition reads with load-graph, etc. etc.<br>
<div><div class="h5">><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> 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 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>
</div></div>> _______________________________________________<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>
<span class="HOEnZb"><font color="#888888"><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>
</font></span></blockquote></div><br></div>