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
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
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