Running MetaVelvet 1.2.01

[seb567]

Hello,

I am assembling 6 datasets with MetaVelvet on a computer that has 128 GB of memory with huge pages enabled in Linux. The purpose is to draw a comparison with Ray Méta.

I am using MetaVelvet 1.2.01 and Velvet 1.1.06, as indicated in the documentation available at http://metavelvet.dna.bio.keio.ac.jp/

I compiled Velvet with MAXKMERLENGTH=51.


I assembled

ERS006494 186073978 sequences
ERS006497 161222460 sequences
ERS006592 26934980 sequences

without errors in the process.


However, I am not enable to assemble these:

SRS011098 202487723 seq.

Reason: velvetg: Can't calloc 18446744072008167979 Annotations totalling 18446744046487413424 bytes: Cannot allocate memory


The range of an unsigned 64-bit integer is 0 to 18446744073709551615.
Therefore, there is a integer overflow.


SRS017227 139002751 seq.

Segmentation fault (core dumped)

(gdb) bt
#0 0x0000000000429f71 in newPreGraph_pg ()
#1 0x000000000040293c in main ()



SRS018661 288475194 seq.

Segmentation fault (core dumped)

(gdb) bt
#0 0x0000000000426940 in importRoadMapArray ()
#1 0x000000000040292f in main ()


Are there things in particular I should check in the input data ?

Are these problems known bugs that were fixed since v1.1.06 ?

Is MetaVelvet 1.2.01 compatible with Velvet 1.2.07 ?


If it can help, my commands for SRS011098 are


velveth SRS011098/velvet-block 51 -fastq -shortPaired SRS011098/block-device.fastq

velvetg SRS011098/velvet-block -exp_cov auto -ins_length 211

meta-velvetg SRS011098/velvet-block -ins_length 211


Thank you for your support.


Sébastien Boisvert

[weijenc]

I am not an expert, but I think the error message suggests that you don't have enough memory to do the assembly?

WJ

[DFJ111]

http://en.wikipedia.org/wiki/Integer_overflow

Is this relevant? Also, if you have to use a page file (i.e. hard drive) for extra memory, it will probably mean the assembly takes far too long because reading into/out of a hard drive is about 100X slower.

[aaronrjex]

I was having a similar problem but my error message was coming up at the coverage estimation stage. It seems that MetaVelvet doesn't compile so well with a kmer limit above 64. If you recompile MetaVelvet and make sure you set your kmer limit to 64, you might solve the issue. It worked for me at least.

[DFJ111]

63. Velvet doesn't like even numbered kmer values (something to do with it not dealing well with palindromes). So you'd never use 64 as an actual kmer value.

[aaronrjex]

Yep sorry that was a typo. I meant 63.

[af1a]

Hi Sébastien Boisvert,

Currently, the last version of MetaVelvet is MetaVelvet version 1.2.02 which is compatible with the last version of Velvet, version 1.2.10.
Anyway, for the error in your case, you need more memory and also the integer type is not enough to process your data (we will revise the type). Thanks a lot for using and trying MetaVelvet.

Best regards,
Afia (currently continue the MetaVelvet project)