soap2 memory requirements

[dara]

Hi all,

Soap2, on its website states that it has a 6.8 GB footprint (when using the human genome as the reference).

Is anyone aware of whether reporting all best hits (option -r 2) has any effect on the memory requirements? When I use the default setting of reporting one of the best hits randomly, SOAP runs without issues. But, when I set this -r 2 option, SOAP gives a segmentation fault.

Anyone else have similar experiences?

Thanks

[Torst]

Is anyone aware of whether reporting all best hits (option -r 2) has any effect on the memory requirements? When I use the default setting of reporting one of the best hits randomly, SOAP runs without issues. But, when I set this -r 2 option, SOAP gives a segmentation fault. Anyone else have similar experiences?

I don't expect a mapping algorithm to need more memory for -r 2 over -r 0 or -r 1 but it will take more CPU time as it has to go through all the hits, not just stop after one.

I also get a segfault when using soap2 with -r 2. A segfault means the process has attempted to access a memory address which has not been allocated to it - usually a pointer bug.

[allo]

Hi, more SOAP,
The SOAP2 paper states that the new SOAP2 supports several input and output formats:
The output formats include a SOAP tab-delimited
text table, a gzipped text table, a Sequence Alignment/Map (SAM)
format and its binary equivalent (BAM) that is recommended by
the 1000 Genomes Consortium, and a Consed format that fits with
the assembly viewer.
Does anybody know how to select those formats? I have not been able to find any infp on the documentation or web site.
Thanks!!