<div dir="ltr">Hi Alexis,<div><br></div><div>One way to get the 'bleeding-edge' branch is to clone it into a fresh directory; for example:</div><div> git clone <a href="http://github.com/ged-lab/khmer.git">http://github.com/ged-lab/khmer.git</a> -b bleeding-edge khmer-BETA</div>
<div><br></div><div>Assuming you already have a clone of the 'ged-lab/khmer' repo, then you should also be able to do:</div><div> git fetch origin</div><div> git checkout bleeding-edge</div><div>Depending on how old your Git client is and what its defaults are, you may have to do the following instead:</div>
<div> git checkout --track -b bleeding-edge origin/bleeding-edge</div><div><br></div><div>Hope this helps,</div><div> Eric</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Mar 12, 2013 at 11:32 AM, Alexis Groppi <span dir="ltr"><<a href="mailto:alexis.groppi@u-bordeaux2.fr" target="_blank">alexis.groppi@u-bordeaux2.fr</a>></span> wrote:<br>
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<div>Le 12/03/2013 16:16, C. Titus Brown a
écrit :<br>
</div><div class="im">
<blockquote type="cite">
<pre>On Tue, Mar 12, 2013 at 04:15:05PM +0100, Alexis Groppi wrote:
</pre>
<blockquote type="cite">
<pre>Hi Titus,
Thanks for your answer
Actually it's my second attempt with filter-below-abund.
The first time, I thought the problem was coming from the location of my
<a href="http://table.kh" target="_blank">table.kh</a> file : in a storage element with poor level performance of I/O
I killed the job after 24h, moved the file in a best place and re run it
But with the same result : no completion after 24h
Any Idea ?
Thanks
Cheers From Bordeaux :)
Alexis
PS : The command line was the following :
./filter-below-abund.py <a href="http://174r1_table.kh" target="_blank">174r1_table.kh</a> 174r1_prinseq_good_bFr8.fasta.keep
Is this correct ?
</pre>
</blockquote>
<pre>Yes, looks right... Can you try with the bleeding-edge branch, which now
incorporates a potential fix for this issue?</pre>
</blockquote></div>
From here : <a href="https://github.com/ged-lab/khmer/tree/bleeding-edge" target="_blank">https://github.com/ged-lab/khmer/tree/bleeding-edge</a> ?<br>
or <br>
here : <a href="https://github.com/ctb/khmer/tree/bleeding-edge" target="_blank">https://github.com/ctb/khmer/tree/bleeding-edge</a> ?<br>
<br>
Do I have to make a fresh install ? and How ?<br>
Or just replace all the files and folders ?<br>
<br>
Thanks :)<br>
<br>
Alexis<div><div class="h5"><br>
<br>
<blockquote type="cite">
<pre>
thanks,
--titus
</pre>
<blockquote type="cite">
<pre>Le 12/03/2013 14:41, C. Titus Brown a ?crit :
</pre>
<blockquote type="cite">
<pre>On Tue, Mar 12, 2013 at 10:48:03AM +0100, Alexis Groppi wrote:
</pre>
<blockquote type="cite">
<pre>Metagenome assembly :
My data :
- original (quality filtered) data : 4463243 reads (75 nt) (Illumina)
1/ Single pass digital normalization with normalize-by-median (C=20)
==> file .keep of 2560557 reads
2/ generated a hash table by load-into-counting on the .keep file
==> file .kh of ~16Go (huge file ?!)
3/ filter-below-abund with C=100 from the two previous file (<a href="http://table.kh" target="_blank">table.kh</a>
and reads.keep)
Still running after 24 hours :(
Any advice to speed up this step ? ... and the others (partitionning ...) ?
I can have an access to a HPC : ~3000 cores.
</pre>
</blockquote>
<pre>Hi Alexis,
filter-below-abund and filter-abund have occasional bugs that prevent them
from completing. I would kill and restart. For that few reads it should
take no more than a few hours to do everything.
Most of what khmer does cannot easily be distributed across multiple chassis,
note.
best,
--titus
</pre>
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<pre>--
</pre>
</blockquote>
<pre></pre>
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<br>
</div></div><span class="HOEnZb"><font color="#888888"><div>-- <br>
<img src="cid:part1.03070403.09070706@u-bordeaux2.fr" border="0"></div>
</font></span></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><div>Eric McDonald</div><div>HPC/Cloud Software Engineer</div><div> for the Institute for Cyber-Enabled Research (iCER)</div><div> and the Laboratory for Genomics, Evolution, and Development (GED)</div>
<div>Michigan State University</div><div>P: 517-355-8733</div></div>
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