Help: velvetg is trying allocate 2251799813685248 bytes
0
0
Entering edit mode
9.0 years ago
scchess ▴ 640

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 • 3.0k views
ADD COMMENT
0
Entering edit mode

What value of kmer did you select in velveth?

ADD REPLY
0
Entering edit mode

51 exactly as recommended in the web site.

ADD REPLY

Login before adding your answer.

Traffic: 3927 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6