Question: Help: velvetg is trying allocate 2251799813685248 bytes
0
gravatar for SmallChess
4.2 years ago by
SmallChess480
Australia
SmallChess480 wrote:

I have a very small data-set for metagenomic. The largest .fa file is about 15349 bytes and there are six of those files.

I am following the instructions on http://metavelvet.dna.bio.keio.ac.jp/MV.html exactly. In particular running velveth to construct a directory of k-mer hash table. It completed immediately most probably because my data set is small enough. Next, I tried running velvetg exactly as shown in the web site. But.. I got

 

-> velvetg DF1 -exp_cov auto -ins_length 260

[0.000000] Reading roadmap file DF1/Roadmaps

[0.000391] 46 roadmaps read

velvetg: Can't calloc 281474976710656 void*s totalling 2251799813685248 bytes: Cannot allocate memory

 

This is clearly nonsense. Does anybody know how to work with the assembler?

 

 

 

 

 

metagenomic velvetg • 1.9k views
ADD COMMENTlink modified 4.2 years ago by Antonio R. Franco4.0k • written 4.2 years ago by SmallChess480
0
gravatar for Antonio R. Franco
4.2 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:

what value of kmer did you select in velveth?

 

ADD COMMENTlink written 4.2 years ago by Antonio R. Franco4.0k

51 exactly as recommended in the web site.

ADD REPLYlink written 4.2 years ago by SmallChess480
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