newbler: out of memory.

[pao205]

I am getting an out of memory error using newbler 2.8
#runAssembly 2.8 (20120726_1306)
I have around 7GB of single end sequencing data from a 65Mb diploid genome. ~16 million reads.
I have a machine with 62Gb memory, so memory requirements should be well within that.
newbler complains it is out of memory even though it is using only ~4GB.

I've seen similar posts, but they just say to rerun, but that does not work for me.

any help would be appreciated.

output is below.

Assembly computation starting at: Wed Apr 24 12:37:57 2013 (v2.8 (20120726_1306))
Building contigs/scaffolds...
-> 12731 large contigs, 19863 all contigs
Computing signals...
-> 10200000 of 50076485...Reading flowgrams...
-> 45600000 of 50076485...Reading flowgrams...
-> 50076485 of 50076485...
Checkpointing...
Generating output...
-> 45600000 of 50076485...Reading flowgrams...
-> 50000000 of 50076485...
Error: The computation ran out of memory and is unable to continue.

[GenoMax]

Are you running into some kind of system resource limit?
Was newbler compiled on this machine?

[pao205]

thanks GenoMax -

Newbler was not compiled on the machine, and it is a 32bit executable.
I think that explains the problem.

I'll get back to Roche to see if they have a 64bit version or can provide the source.

thanks for the nudge in the right direction.

[pao205]

In case someone else finds this useful

use linux command 'file runAssembly'
#file ../apps/mapper/bin/runAssembly
../apps/mapper/bin/runAssembly: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.4.3, not stripped

compare with a 64bit executable of version 2.7
#file runAssembly
runAssembly: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.4.3, not stripped

the latter version worked with my data.