Help: velvetg is trying allocate 2251799813685248 bytes
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6.5 years ago
SmallChess ▴ 550

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?

 

 

 

 

 

velvetg metagenomic • 2.4k views
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6.5 years ago

what value of kmer did you select in velveth?

 

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51 exactly as recommended in the web site.

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