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Hi,<br>
<br>
Metagenome assembly : <br>
My data : <br>
- original (quality filtered) data : 4463243 reads (75 nt)
(Illumina)<br>
1/ Single pass digital normalization with normalize-by-median (C=20)<br>
==> file .keep of 2560557 reads<br>
2/ generated a hash table by load-into-counting on the .keep file<br>
==> file .kh of ~16Go (huge file ?!)<br>
3/ filter-below-abund with C=100 from the two previous file
(table.kh and reads.keep)<br>
Still running after 24 hours :(<br>
<br>
Any advice to speed up this step ? ... and the others (partitionning
...) ?<br>
<br>
I can have an access to a HPC : ~3000 cores.<br>
<br>
Thanks for your help<br>
<br>
Alexis<br>
<br>
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<img src="cid:part1.07000309.08070007@u-bordeaux2.fr" border="0"></div>
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