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Hi Titus,<br>
<br>
Thanks for your answer<br>
Actually it's my second attempt with filter-below-abund.<br>
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<br>
I killed the job after 24h, moved the file in a best place and re
run it<br>
But with the same result : no completion after 24h<br>
<br>
Any Idea ?<br>
<br>
Thanks<br>
<br>
Cheers From Bordeaux :)<br>
<br>
Alexis<br>
<br>
PS : The command line was the following :
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<pre style="color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium;">./filter-below-abund.py 174r1_table.kh 174r1_prinseq_good_bFr8.fasta.keep
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Is this correct ?<br>
<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">Le 12/03/2013 14:41, C. Titus Brown a
écrit :<br>
</div>
<blockquote cite="mid:20130312134137.GE32589@idyll.org" type="cite">
<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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<br>
<div class="moz-signature">-- <br>
<img src="cid:part1.06080704.00080303@u-bordeaux2.fr" border="0"></div>
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