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<div class="moz-cite-prefix">Le 12/03/2013 16:16, C. Titus Brown a
écrit :<br>
</div>
<blockquote cite="mid:20130312151635.GB8145@idyll.org" type="cite">
<pre wrap="">On Tue, Mar 12, 2013 at 04:15:05PM +0100, Alexis Groppi wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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
table.kh 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 174r1_table.kh 174r1_prinseq_good_bFr8.fasta.keep
Is this correct ?
</pre>
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<pre wrap="">
Yes, looks right... Can you try with the bleeding-edge branch, which now
incorporates a potential fix for this issue?</pre>
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From here : <a class="moz-txt-link-freetext" href="https://github.com/ged-lab/khmer/tree/bleeding-edge">https://github.com/ged-lab/khmer/tree/bleeding-edge</a> ?<br>
or <br>
here : <a class="moz-txt-link-freetext" href="https://github.com/ctb/khmer/tree/bleeding-edge">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<br>
<br>
<blockquote cite="mid:20130312151635.GB8145@idyll.org" type="cite">
<pre wrap="">
thanks,
--titus
</pre>
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<pre wrap="">Le 12/03/2013 14:41, C. Titus Brown a ?crit :
</pre>
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<pre wrap="">On Tue, Mar 12, 2013 at 10:48:03AM +0100, Alexis Groppi wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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 (table.kh
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 wrap="">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
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<pre wrap="">
--
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</pre>
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<div class="moz-signature">-- <br>
<img src="cid:part1.03070403.09070706@u-bordeaux2.fr" border="0"></div>
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