Re: [Seqan-dev] razers3 memory problem

[Matthias Lienhard <lienhard@molgen.mpg.de>]

Hi Dave,

I see. Is it planned, that the reads are processed in blocks internally? 
10M reads is not really a realistic input size these days, and I 
imagine, a lot of potential users are scared off, when the program (or 
worse: the server) crashes.
Also, it is not really a practical solution to split the files, as 
handling the data is difficult enough.

Best, Matthias

On 06/07/13 09:16, Weese, David wrote:
> 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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