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dzerbino / velvet

Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18: 821-829
https://europepmc.org/article/pmc/2336801
GNU General Public License v2.0
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error in increasing Kmer lenght from 31 to 51 #42

Closed shrutidabral closed 6 years ago

shrutidabral commented 6 years ago

I want to run velevth on 51 kmer but i am getting error.

I tried to do these commandmake cleanmake MAXKMERLENGTH=51 make velveth velvetg

I try to run command still it gives [0.000000] Velvet can't handle k-mers as long as 33! We'll stick to 31 if you don't mind.

when I try to print velveth command I get the following message:

velveth - simple hashing programVersion 1.2.09

Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)This is free software; see the source for copying conditions. There is NOwarranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Compilation settings:CATEGORIES = 2MAXKMERLENGTH = 31

I also check installation for zlib . this is up to date . Any help would be appreciated! thankyou

jmarshall commented 6 years ago

For velvet, just run make only once:

make MAXKMERLENGTH=51

Velvet has a somewhat unusual makefile whose default target does a full clean and rebuild, which is convenient for the one-shot builds that most users are doing.

Incidentally, you appear not to be using the final version of velvet (1.2.10) or the code in this git repository, which contains a couple of additional small fixes.

shrutidabral commented 6 years ago

Thankyou for your kind consideration. :+1: