Re: [Seqan-dev] razers3 memory problem

["Weese, David" <weese@campus.fu-berlin.de>]

Hi Matthias,

RazerS keeps a q-gram index of reads in memory. Hence its memory consumption is directly proportional to the input size. And it requires about 10GB for 10M x 100bp reads. Unfortunately, there is currently no other option than to split the input file into chunks and map then independently one-after-another or in-parallel on a cluster.

BAM outputs will certainly be supported in the near future and gzipped fastq input could be supported but requires to benchmark the alternative I/O module before.

Cheers,
Dave

--
David Weese                     weese@inf.fu-berlin.de
Freie Universität Berlin        http://www.inf.fu-berlin.de/
Institut für Informatik         Phone: +49 30 838 75137
Takustraße 9                    Algorithmic Bioinformatics
14195 Berlin                    Room 020

Am 05.06.2013 um 11:44 schrieb Matthias Lienhard <lienhard@molgen.mpg.de>:

> Hi,
> when runnig razers3 on my paired end HiSeq fastq files I get the following errors
> 
> 
> razers3 -i 94 -rr 95 -tc 20 -o sample.sam reads1.fastq reads2.fastq
> terminate called recursively
> terminate called recursively
> Aborted
> 
> or
> 
> terminate called after throwing an instance of 'std::bad_alloc'
>  what():  std::bad_alloc
> Aborted
> 
> It seems as memory usage is very high (>50gb). Each of the fastq files is about 7 gb. When I take the first 100000 reads, the razers3 seems to work fine. However, I don't want to split the files in small chucks and merge them together afterwards (because of disk usage and convenience - I have about 50 samples to process)
> Is there another way to handle this issue?
> 
> Also, it would be very convienient if gzipped fastq files could be used as input directly - and output in bam-format would be nice as well.
> 
> Best wishes, Matthias
> 
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