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Hi Eric,<br>
<br>
Thanks for your answer.<br>
But unfortunately, after many attempts I'm getting this error :<tt><br>
<br>
</tt><tt>starting threads</tt><tt><br>
</tt><tt>starting writer</tt><tt><br>
</tt><tt>loading...</tt><tt><br>
</tt><tt>... filtering 0</tt><tt><br>
</tt><tt>/var/lib/torque/mom_priv/jobs/2693.rainman.SC: line 46:
63657 Floating point exception(core dumped)
./khmer-BETA/sandbox/filter-below-abund.py
/scratch/ag/khmer/174r1_table.kh
/mnt/var/home/ag/174r1_prinseq_good_bFr8.fasta.keep</tt><tt><br>
</tt><tt><br>
</tt><tt>real 3m30.163s</tt><tt><br>
</tt><tt>user 0m0.088s</tt><br>
<br>
Your opinion ?<br>
<br>
Thanks<br>
<br>
Alexis<br>
<br>
<br>
<div class="moz-cite-prefix">Le 13/03/2013 00:55, Eric McDonald a
écrit :<br>
</div>
<blockquote
cite="mid:CAGhFaV2QBHq_+rOU-3kC1h=ynVj+PvNVRRjyE4JjmmsRSa9cYA@mail.gmail.com"
type="cite">
<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 moz-do-not-send="true"
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 moz-do-not-send="true"
href="mailto:alexis.groppi@u-bordeaux2.fr" target="_blank">alexis.groppi@u-bordeaux2.fr</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> <br>
<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 moz-do-not-send="true" 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 moz-do-not-send="true" 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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true" 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>
</blockquote>
<pre>--
</pre>
</blockquote>
</blockquote>
<br>
</div>
</div>
<span class="HOEnZb"><font color="#888888">
<div>-- <br>
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border="0"></div>
</font></span></div>
<br>
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</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>
</div>
</blockquote>
<br>
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