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Old 05-13-2009, 12:59 PM   #1
dara
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Location: texas

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Default soap2 memory requirements

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
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Old 05-13-2009, 06:11 PM   #2
Torst
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Location: The University of Melbourne, AUSTRALIA

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Default

Quote:
Originally Posted by dara View Post
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.
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Old 07-07-2009, 04:40 PM   #3
allo
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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!!
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